diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index e8b7e999b..ee7c36b6f 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 30 06:26:55 2024Mon Sep 23 06:26:44 2024
1ToolsetMon Sep 30 18:33:17 2024Mon Sep 23 18:33:07 2024
2ToolsetTue Oct 01 06:27:45 2024Tue Sep 24 06:26:56 2024
3ToolsetTue Oct 01 18:32:45 2024Tue Sep 24 18:32:18 2024
4ToolsetWed Oct 02 06:26:14 2024Wed Sep 25 06:26:23 2024
5ToolsetWed Oct 02 18:33:18 2024Wed Sep 25 18:31:33 2024
6ToolsetThu Oct 03 06:26:03 2024Thu Sep 26 06:25:57 2024
7ToolsetThu Oct 03 18:32:58 2024Thu Sep 26 18:30:44 2024
8ToolsetFri Oct 04 06:26:37 2024Fri Sep 27 06:27:02 2024
9ToolsetFri Oct 04 18:32:34 2024Fri Sep 27 18:32:42 2024
10ToolsetSat Sep 28 06:25:48 2024Sat Sep 21 06:25:16 2024
11ToolsetSat Sep 28 18:31:23 2024Sat Sep 21 18:31:38 2024
12ToolsetSun Sep 29 06:24:45 2024Sun Sep 22 06:25:20 2024
13ToolsetSun Sep 29 18:31:20 2024Sun Sep 22 18:31:24 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 30 06:26:55 2024Mon Sep 23 06:26:44 2024
1ToolsetMon Sep 30 18:33:17 2024Mon Sep 23 18:33:07 2024
2ToolsetTue Oct 01 06:27:45 2024Tue Sep 24 06:26:56 2024
3ToolsetTue Oct 01 18:32:45 2024Tue Sep 24 18:32:18 2024
4ToolsetWed Oct 02 06:26:14 2024Wed Sep 25 06:26:23 2024
5ToolsetWed Oct 02 18:33:18 2024Wed Sep 25 18:31:33 2024
6ToolsetThu Oct 03 06:26:03 2024Thu Sep 26 06:25:57 2024
7ToolsetThu Oct 03 18:32:58 2024Thu Sep 26 18:30:44 2024
8ToolsetFri Oct 04 06:26:37 2024Fri Sep 27 06:27:02 2024
9ToolsetFri Oct 04 18:32:34 2024Fri Sep 27 18:32:42 2024
10ToolsetSat Oct 05 06:25:14 2024Sat Sep 28 06:25:48 2024
11ToolsetSat Sep 28 18:31:23 2024Sat Sep 21 18:31:38 2024
12ToolsetSun Sep 29 06:24:45 2024Sun Sep 22 06:25:20 2024
13ToolsetSun Sep 29 18:31:20 2024Sun Sep 22 18:31:24 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 80961f455..e88625804 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -63,11 +63,11 @@ "date2": "Fri Sep 27 18:32:42 2024" }, "10": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-28-06-10-1/results.html", - "date1": "Sat Sep 28 06:25:48 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-28-06-10-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-21-06-10-1/results.html", - "date2": "Sat Sep 21 06:25:16 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html", + "date1": "Sat Oct 05 06:25:14 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-28-06-10-1/results.html", + "date2": "Sat Sep 28 06:25:48 2024" }, "12": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-29-06-10-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.json new file mode 100644 index 000000000..57bc13d89 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.json @@ -0,0 +1,7 @@ +{ + "10": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html", + "date1": "Sat Oct 05 06:25:14 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.txt new file mode 100644 index 000000000..93c7a3f31 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.txt @@ -0,0 +1,25 @@ +-t datamash_transpose --tool-version ac092723240d +-t deeptools_plot_fingerprint --tool-version 2da482e408b8 +-t umi_tools_extract --tool-version 6a675c3aa610 +-t umi_tools_extract --tool-version 99aea37a7ff7 +-t umi_tools_extract --tool-version f3759eec3018 +-t bwa --tool-version 3fe632431b68 +-t medaka_variant_pipeline --tool-version 336b3def9b2b +-t poretools_qualdist --tool-version ae9060e764b5 +-t featurecounts --tool-version 38b6d12edc68 +-t featurecounts --tool-version f3a5f075498f +-t samtools_fixmate --tool-version bc0cc7bfbfe9 +-t sam_to_bam --tool-version cf1ffd88f895 +-t chromeister --tool-version e483be1014b6 +-t slice_image --tool-version 8856a7c85e4c +-t scanpy_read_10x --tool-version c8391a25dee3 +-t scanpy_read_10x --tool-version d92e6f12b790 +-t scanpy_run_tsne --tool-version 384cacc40611 +-t scanpy_run_tsne --tool-version 8eff7ec034e3 +-t add_input_name_as_column --tool-version 3284b72eef56 +-t lofreq_filter --tool-version 7dfca164d2e3 +-t bcftools_query_list_samples --tool-version ed4ea9de1791 +-t bcftools_isec --tool-version 02f349bdbf96 +-t vcfannotate --tool-version 01e0321aca98 +-t vcfrandomsample --tool-version 6257ee3b50d3 +-t ivar_getmasked --tool-version 2cf4a1cafc16 diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/066e0eaa4712a55e.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/066e0eaa4712a55e.json new file mode 100644 index 000000000..bce32bbec --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/066e0eaa4712a55e.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "066e0eaa4712a55e", + "history_id": "779d4cab783f0ad5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:45:26.565484", + "update_time": "2024-10-05T06:45:32.749018", + "galaxy_version": "24.1", + "external_id": "gxy-zmnpq", + "handler": null, + "job_runner_name": null, + "command_line": "poretools qualdist '/galaxy/server/database/objects/a/7/4/dataset_a74e2bbb-94df-4176-bcac-cda666391a8a.dat' > '/galaxy/server/database/objects/6/b/b/dataset_6bb58ad4-0dd4-44b1-a170-0b2e6aac5738.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fast5.tar\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"" + }, + "inputs": { + "input": { + "id": "40224001529b2140", + "src": "hda", + "uuid": "a74e2bbb-94df-4176-bcac-cda666391a8a" + } + }, + "outputs": { + "output": { + "id": "4b7e4165841ed691", + "src": "hda", + "uuid": "6bb58ad4-0dd4-44b1-a170-0b2e6aac5738" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/2704ccb375827a9b.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/2704ccb375827a9b.json new file mode 100644 index 000000000..73a335ab7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/2704ccb375827a9b.json @@ -0,0 +1,65 @@ +{ + "model_class": "Job", + "id": "2704ccb375827a9b", + "history_id": "779d4cab783f0ad5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:40:17.162455", + "update_time": "2024-10-05T06:40:23.333336", + "galaxy_version": "24.1", + "external_id": "gxy-7nbzx", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/b/9/9/dataset_b99998c9-5079-466a-bd90-6b4ac47ef392.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/e/f/d/dataset_efd26cbf-3208-4678-be8b-be73c00f4356.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/5/1/b/dataset_51bc75bf-3db8-4f22-9b83-0177410c5511.dat' && mv out2.gz '/galaxy/server/database/objects/c/8/5/dataset_c850d4a7-42a1-430b-81e0-4ea7da635e32.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "log": "false", + "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", + "error_correct_cell": "false", + "blacklist": null, + "whitelist": null, + "ignore_read_pair_suffixes": "false", + "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", + "input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"NNNNNNCCCCCC\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 87, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}" + }, + "inputs": { + "input_type_cond|input_read1": { + "id": "75502bcd39344a71", + "src": "hda", + "uuid": "b99998c9-5079-466a-bd90-6b4ac47ef392" + }, + "input_type_cond|input_read2": { + "id": "20a79f958a1ad4a1", + "src": "hda", + "uuid": "efd26cbf-3208-4678-be8b-be73c00f4356" + } + }, + "outputs": { + "out": { + "id": "db5a2d4573973b22", + "src": "hda", + "uuid": "51bc75bf-3db8-4f22-9b83-0177410c5511" + }, + "out2": { + "id": "1901d0f883d04f28", + "src": "hda", + "uuid": "c850d4a7-42a1-430b-81e0-4ea7da635e32" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/39a53760c56001e8.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/39a53760c56001e8.json new file mode 100644 index 000000000..f62cfdeb6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/39a53760c56001e8.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "39a53760c56001e8", + "history_id": "779d4cab783f0ad5", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:28:02.222110", + "update_time": "2024-10-05T06:28:15.264725", + "galaxy_version": "24.1", + "external_id": "gxy-qdt55", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/6/registry.xml' '/galaxy/server/database/jobs_directory/000/6/upload_params.json' '6:/galaxy/server/database/objects/1/e/0/dataset_1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f_files:/galaxy/server/database/objects/1/e/0/dataset_1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_a0kkzha3\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bowtie2 test1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_tmkk73t3\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "39a53760c56001e8", + "src": "hda", + "uuid": "1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/3bdef6d60132b40e.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/3bdef6d60132b40e.json new file mode 100644 index 000000000..ae5ac0350 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/3bdef6d60132b40e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "3bdef6d60132b40e", + "history_id": "779d4cab783f0ad5", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:53:35.229647", + "update_time": "2024-10-05T06:53:47.319910", + "galaxy_version": "24.1", + "external_id": "gxy-nlk7h", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/116/registry.xml' '/galaxy/server/database/jobs_directory/000/116/upload_params.json' '160:/galaxy/server/database/objects/5/5/8/dataset_55886639-e887-4ce9-a9d5-0619bc31ea48_files:/galaxy/server/database/objects/5/5/8/dataset_55886639-e887-4ce9-a9d5-0619bc31ea48.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_6tbgvd3j\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"3_reverse_read_pp_lt.sam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_w_rdbek2\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "6d0793221f983d04", + "src": "hda", + "uuid": "55886639-e887-4ce9-a9d5-0619bc31ea48" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/57809ef5376e1992.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/57809ef5376e1992.json new file mode 100644 index 000000000..58ec8f04e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/57809ef5376e1992.json @@ -0,0 +1,62 @@ +{ + "model_class": "Job", + "id": "57809ef5376e1992", + "history_id": "779d4cab783f0ad5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:27:29.567735", + "update_time": "2024-10-05T06:28:01.140320", + "galaxy_version": "24.1", + "external_id": "gxy-dsdtv", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/1/0/4/metadata_104947e0-34a1-43e1-8db9-1cc069aafbe0.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat' './1.bam' && ln -s 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\"orderMatters\": \"No\"}" + }, + "inputs": { + "multibam_conditional|bamfiles": { + "id": "1e4681385ecc7453", + "src": "hda", + "uuid": "b79efeae-155c-4cc8-bbba-283551a339c4" + }, + "multibam_conditional|bamfiles1": { + "id": "1e4681385ecc7453", + "src": "hda", + "uuid": "b79efeae-155c-4cc8-bbba-283551a339c4" + }, + "multibam_conditional|bamfiles2": { + "id": "1e4681385ecc7453", + "src": "hda", + "uuid": "b79efeae-155c-4cc8-bbba-283551a339c4" + } + }, + "outputs": { + "outFileName": { + "id": "57809ef5376e1992", + "src": "hda", + "uuid": "5d34d069-292e-4b2d-a397-db6ed9e61c4c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/8b790c9bf7dcddba.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/8b790c9bf7dcddba.json new file mode 100644 index 000000000..81bd201ad --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/8b790c9bf7dcddba.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8b790c9bf7dcddba", + "history_id": "779d4cab783f0ad5", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T07:01:37.792525", + "update_time": "2024-10-05T07:01:49.985880", + "galaxy_version": "24.1", + "external_id": "gxy-27wfq", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/144/registry.xml' '/galaxy/server/database/jobs_directory/000/144/upload_params.json' 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Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/b3289f59ef3f0719.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/b3289f59ef3f0719.json new file mode 100644 index 000000000..8d2e416a4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/b3289f59ef3f0719.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "b3289f59ef3f0719", + "history_id": "779d4cab783f0ad5", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T07:06:42.537443", + "update_time": "2024-10-05T07:06:55.045087", + "galaxy_version": "24.1", + "external_id": "gxy-nxf4z", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/161/registry.xml' 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"uuid": "0c2059cc-0f54-488d-8266-34305b8c22e5" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/d9efec2f13a62343.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/d9efec2f13a62343.json new file mode 100644 index 000000000..0a4af5ce8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/d9efec2f13a62343.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d9efec2f13a62343", + "history_id": "779d4cab783f0ad5", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:31:26.620053", + "update_time": "2024-10-05T06:31:38.502256", + "galaxy_version": "24.1", + "external_id": "gxy-2r224", + "handler": null, + "job_runner_name": null, + 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\"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "e74073ea01a7986a", + "src": "hda", + "uuid": "891c62e7-39a8-47bd-9982-130c20cb4662" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/db5a2d4573973b22.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/db5a2d4573973b22.json new file mode 100644 index 000000000..e4a53eb2e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/db5a2d4573973b22.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "db5a2d4573973b22", + "history_id": "779d4cab783f0ad5", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": 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\"file_data\": \"/galaxy/server/database/tmp/upload_file_data_sa7me2aa\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"gff\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "9f979cc9eed714b5", + "src": "hda", + "uuid": "0baaabba-42cc-4a33-b831-6cf2d8c991c7" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/f43133f4c6d4bc45.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/f43133f4c6d4bc45.json new file mode 100644 index 000000000..3b95be8ad --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/f43133f4c6d4bc45.json @@ -0,0 +1,51 @@ +{ + "model_class": "Job", + "id": "f43133f4c6d4bc45", + "history_id": "779d4cab783f0ad5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:54:09.839900", + "update_time": "2024-10-05T06:54:14.906118", + "galaxy_version": "24.1", + "external_id": "gxy-k9dxb", + "handler": null, + "job_runner_name": null, + "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/a/4/2/dataset_a427b668-df70-4d93-bf0d-7e8f425d70f4.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/e/6/2/dataset_e62778dc-6e69-4eec-bae3-03bd673dd5f0.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"sam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "addms": "false", + "tempcigar": "false", + "noprop": "false", + "remsec": "false" + }, + "inputs": { + "bamfile": { + "id": "b3289f59ef3f0719", + "src": "hda", + "uuid": "a427b668-df70-4d93-bf0d-7e8f425d70f4" + } + }, + "outputs": { + "output": { + "id": "88ff02288943c7b4", + "src": "hda", + "uuid": "e62778dc-6e69-4eec-bae3-03bd673dd5f0" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/faa5496b14d1cee0.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/faa5496b14d1cee0.json new file mode 100644 index 000000000..7f5da1480 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/faa5496b14d1cee0.json @@ -0,0 +1,45 @@ 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"\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"isec.b.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fu4yz2rn\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "e5762793e1ff0a7b", + "src": "hda", + "uuid": "b66abd4d-5959-48c5-b442-99aab280fd23" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/fdadf5367d57b093.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/fdadf5367d57b093.json new file mode 100644 index 000000000..0fc832026 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/fdadf5367d57b093.json @@ -0,0 +1,74 @@ +{ + "model_class": "Job", + "id": "fdadf5367d57b093", + "history_id": "779d4cab783f0ad5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-10-05T06:39:01.305001", + "update_time": "2024-10-05T06:39:08.059295", + "galaxy_version": "24.1", + "external_id": "gxy-fkj9h", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/9/0/5/dataset_9050a585-8a74-41a8-9213-a845d72b8a4b.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/0/e/7/dataset_0e75abdf-ef93-4d07-a77a-6d9a90d7af68.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='CCCCCCNNNNNNNNNN' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/f/3/d/dataset_f3dd47d3-ba44-41ec-9ce4-e6b17f0835e0.dat' False --log='/galaxy/server/database/objects/4/7/d/dataset_47d28eae-9b16-4d6b-9324-42de7593b94e.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/5/b/0/dataset_5b0e5b07-26f7-4cd1-b6b9-f4af1b4a8c0d.dat' && mv out2.gz '/galaxy/server/database/objects/c/2/8/dataset_c288a374-62c3-404b-a1fd-f562537dc804.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "log": "true", + "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", + "error_correct_cell": "false", + "blacklist": null, + "ignore_read_pair_suffixes": "false", + "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", + "input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"CCCCCCNNNNNNNNNN\", 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'interactivetools_map' option are now relative to 'data_dir', remove the leading 'database/' to suppress this warning: database/interactivetools_map.sqlite +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +DEBUG:yacman.yacman:Patching yaml loader +DEBUG:yacman.yacman1:Using yacman version 0.9.3 +DEBUG:yacman.yacman_future:Using yacman version 0.9.3 +DEBUG:galaxy.app:python path is: /galaxy/server/scripts, /galaxy/server/lib, /galaxy/server/lib, /usr/local/lib/python312.zip, /usr/local/lib/python3.12, /usr/local/lib/python3.12/lib-dynload, /galaxy/server/.venv/lib/python3.12/site-packages +DEBUG:galaxy.config:Configuration directory is /galaxy/server/config +DEBUG:galaxy.config:Data directory is /galaxy/server/database +DEBUG:galaxy.config:Managed config directory is /galaxy/server/config +WARNING:galaxy.config:Paths for the 'interactivetools_map' option are now relative to 'data_dir', remove the leading 'database/' to suppress this warning: database/interactivetools_map.sqlite +WARNING:galaxy.config:Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +WARNING:galaxy.config:Config option 'containers_resolvers_config_file' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file. +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your galaxy database is up-to-date +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your tool shed install database is up-to-date +INFO:galaxy.app:Install database targeting Galaxy's database configuration. +WARNING:galaxy.security.vault:No vault configured. We recommend defining the vault_config_file setting in galaxy.yml +DEBUG:galaxy.web_stack:WeblessApplicationStack initialized +DEBUG:galaxy.web_stack:Will attach to pool(s): job-handlers +galaxy.jobs DEBUG 2024-10-05 06:23:00,502 [pN:job_handler_0,p:8,tN:MainThread] Read job configuration from file: /galaxy/server/config/job_conf.yml +galaxy.jobs INFO 2024-10-05 06:23:00,502 [pN:job_handler_0,p:8,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2024-10-05 06:23:00,502 [pN:job_handler_0,p:8,tN:MainThread] Tag [_default_] handlers: job_handler_0 +galaxy.web_stack.handlers DEBUG 2024-10-05 06:23:00,503 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'tpv_dispatcher' +galaxy.jobs DEBUG 2024-10-05 06:23:00,503 [pN:job_handler_0,p:8,tN:MainThread] Done loading job configuration +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,217 [pN:job_handler_0,p:8,tN:MainThread] Loading datatypes from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,219 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,219 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,219 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,219 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,219 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,220 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,220 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,220 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,220 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,220 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,221 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,222 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,223 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,223 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,223 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,224 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,224 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,224 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,224 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,224 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,224 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,225 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,225 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,225 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,225 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,225 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,225 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,226 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,227 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,228 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,228 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,228 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,228 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,228 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,229 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,230 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,230 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,230 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,230 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,230 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,230 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,231 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,231 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,231 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,231 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,232 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,233 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,233 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,233 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,233 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,233 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,234 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,234 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,235 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,235 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,235 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,235 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,235 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,235 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,236 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,236 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,236 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,236 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,236 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,236 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,237 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,238 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,239 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,239 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,239 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,239 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,239 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_ktab. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,239 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_hist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,240 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_prof. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,240 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Numpy from the datatype registry for extension npy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,364 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,365 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,366 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,367 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,368 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,369 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,370 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,371 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,372 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,373 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,374 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,375 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,378 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,378 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,378 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,378 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,378 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,378 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,379 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,380 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,381 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,382 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,383 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,384 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,385 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,386 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,387 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,388 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,389 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveXz from the datatype registry for extension fast5.tar.xz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pod5 from the datatype registry for extension pod5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,390 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,391 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,392 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,393 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,394 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension colab.tar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,395 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,396 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,397 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,398 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,399 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,400 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,400 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,400 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,400 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,400 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,400 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension 4dn_pairs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension 4dn_pairsam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,401 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,402 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,402 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,402 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,402 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,402 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,403 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,404 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,405 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,406 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,407 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,408 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,409 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,410 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,411 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,412 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,413 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,414 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,417 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,420 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,420 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,421 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,421 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,421 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,421 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,422 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,423 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,424 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,426 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,426 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,428 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,428 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,428 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,428 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,428 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,428 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,429 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,429 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Sbol from the datatype registry for extension sbol. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,429 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,429 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,429 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension docx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,429 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,430 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,430 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,430 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,430 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,430 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,430 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,431 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,431 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,431 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,431 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,431 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,431 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,432 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,432 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,432 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,432 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,432 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,433 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,433 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,433 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,433 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,433 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,434 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,434 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,434 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,434 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,435 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,435 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,435 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,435 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,435 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,436 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,436 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,436 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,436 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,436 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,437 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,437 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,437 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,437 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,437 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,438 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,438 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,438 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,438 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,438 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,438 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,439 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,439 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,439 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,439 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,440 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,440 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,440 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,440 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,441 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,441 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,441 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,441 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,441 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,442 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,442 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,442 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,443 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,443 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,443 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,443 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,444 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,444 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,444 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,445 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,445 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,445 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,445 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,445 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,445 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,446 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,446 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,446 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,447 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,447 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,447 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,447 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,448 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,449 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,449 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,450 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,450 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,450 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,450 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,451 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,451 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,451 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,451 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,452 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,452 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,452 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,453 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,453 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,453 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,453 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,453 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,454 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,454 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,454 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,455 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,455 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,455 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,455 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,455 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,455 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,456 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,456 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,456 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,456 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,457 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,457 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,457 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,458 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,458 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,458 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,458 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,458 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,459 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,459 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,459 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,461 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,461 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,461 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,461 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,461 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,462 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,462 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,462 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,462 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,465 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,465 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,465 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,466 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,466 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,466 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,466 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,466 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,474 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,474 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,474 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,474 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,474 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,475 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,475 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,475 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,475 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,475 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,475 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,484 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,484 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,500 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Ogg from the datatype registry for extension ogg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wma from the datatype registry for extension wma. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Webm from the datatype registry for extension webm. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mov from the datatype registry for extension mov. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Avi from the datatype registry for extension avi. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wmv from the datatype registry for extension wmv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,503 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,503 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,503 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,504 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,504 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,504 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,504 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,505 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,505 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,505 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,505 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,505 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,505 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Overriding conflicting datatype with extension 'stl', using datatype from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chain:Net from the datatype registry for extension ucsc.net. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveXz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pod5' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Numpy' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.chain:Net' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Sbol' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,537 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Ogg' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mov' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Avi' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wmv' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wma' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Webm' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ucsc': /cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt with display sites: ['main', 'archaea', 'ucla'] +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'gbrowse': /galaxy/server/tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['wormbase', 'tair', 'modencode_worm', 'modencode_fly'] +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl': /galaxy/server/tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl_data_url': /galaxy/server/tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'igv': /galaxy/server/tool-data/shared/igv/igv_build_sites.txt.sample +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:01,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'rviewer': /galaxy/server/tool-data/shared/rviewer/rviewer_build_sites.txt.sample +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-10-05 06:23:01,550 [pN:job_handler_0,p:8,tN:MainThread] Loading references to tool sheds from internal default config +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-10-05 06:23:01,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed +galaxy.web_stack DEBUG 2024-10-05 06:23:01,552 [pN:job_handler_0,p:8,tN:MainThread] server_name set to: job_handler_0 +galaxy.queue_worker INFO 2024-10-05 06:23:01,555 [pN:job_handler_0,p:8,tN:MainThread] Initializing job_handler_0 Galaxy Queue Worker on amqp://default_user_1fhA0v6Rxss4qx0R-vf:********@edge-24-10-05-06-10-1-galaxy-rabbitmq-server:5672 +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,568 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/78bbd17d0703/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/7fe36019c073/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,569 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/2cf4a1cafc16/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/f95f403841ad/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/d6dc477167f8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/672b6c02fbc7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,570 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/365325116147/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/fec517907949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/c077f71d351f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/ed4ea9de1791/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/dfef7a353ed0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,571 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/01d6b7d6365e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/8abfcd1a6949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/4813f99d81b7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0dbff46d5a1b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,572 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bf235558f2cf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/d40d4bf05718/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/b8e9da766b0f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/776ad0b21536/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/9ef52d95114b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,573 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/b17394940c7a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/582f8b13873d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bf7d6acd9884/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/02f349bdbf96/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/e03f2f3ac3a9/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,574 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/b76adb2f1c51/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/072f606e2e69/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/23680a42e149/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/6ca7c55a27e8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,575 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/fdd127bd4a32/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/403553ae19f6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/5c232a738c74/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/c9c5718edc19/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bdfdf5f6e950/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,576 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/2968c6916579/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/a3dea556218d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/29f9b782727e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/17096387c0e6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,577 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/166c4f50525f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,578 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "all_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,579 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/4542035c1075/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/f54f5baedfdd/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/09b2cdb7ace5/bowtie2_indices.loc' for tool data table 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/3fe632431b68/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bwameth/29bdbc353f20/bwameth_indexes.loc' for tool data table 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwameth_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/e7f19d6a9af8/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/43815fa60f3a/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/a7228a7ea146/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/336b3def9b2b/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,581 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/db25ec99c3ea/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/cc05793bb896/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/a8f343909c17/sailfish_indexes.loc' for tool data table 'sailfish_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sailfish_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/26371a1df031/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/stringtie/1ebd14235b92/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/b72793637686/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/a3b4ad6858ff/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/4d343c1f606b/sam_fa_indices.loc' for tool data table 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sam_fa_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/145f6d74ff5e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,583 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/06dc50b7b711/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/fa7ad9b89f4a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/cf1ffd88f895/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/e1461b5c52a0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,584 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/aa35ee7f3ab2/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/426d707dfc47/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/7dfca164d2e3/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/09d6e4693887/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,585 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/ef2c525bd8cd/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/d12a810c837e/snpeff_msigdb_database.loc' for tool data table 'snpeff_msigdb_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeff_msigdb_database' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/4e21e4f2bc48/snpsift_dbnsfps.loc' for tool data table 'snpsift_dbnsfps' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpsift_dbnsfps' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,586 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/2b62154e39c8/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/e4c01dcece8b/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,587 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/88c07fc4024c/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/c772497b2c32/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,588 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/eec9494fdafa/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/ecb9ea6269ee/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,589 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,590 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/2055c2667eb3/rnastar_index2.loc' for tool data table 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,590 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,590 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,590 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,590 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,590 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/24c5d43cb545/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,591 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/135b80fb1ac2/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/980d2a2e1180/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b502c227b5e6/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/f4af63aaf57a/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,592 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c5e2e5902201/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/660cffd8d92a/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,593 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/e188dc7a68e6/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/a1f0b3f4b781/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,594 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,595 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b9fbec5ac6b2/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,595 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,595 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/61ee47027bd3/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,595 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,595 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,595 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/d080005cffe1/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/5826298f6a73/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/0dbf49c414ae/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,596 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/4805fe3d8fda/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/65432c3abf6c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/2270a8b83c12/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/cf61daf064fe/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,597 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/c2a413e47fe9/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/4c5f4e9b1931/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/77a1e60fd1de/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/666f60a9331a/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,598 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/a5937157062f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/156b60c1530f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/64e2edfe7a2c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/64e2edfe7a2c/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/64e2edfe7a2c/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/a60c359ec43c/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/e4c7985d4585/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/c929a006727f/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/c06951d10364/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/07418a30ed01/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/26983857c91a/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/e479c7ca5570/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/01fb6a7654e6/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/137c4beed34b/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/bad3ca889618/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/231994413f89/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/4431f39ede55/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/4ed32329e0ed/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/443d9a9d6d11/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/0e49b109abc2/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/6662b1a8d326/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/5eb7e84243f2/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/aa784cb3810d/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/36b848d5f3ec/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/c4bde687c846/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/5cc34c3f440d/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/d5ceb9f3c25b/bowtie2_indices.loc' for tool data table 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/2477830927ec/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bwameth/cf1322aeb137/bwameth_indexes.loc' for tool data table 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwameth_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/37b497aa133f/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/4014de1b6daf/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/b0f2be869d6d/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/42ce70172b72/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/45795f582ae9/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/eb746fa6f514/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/fc8804320156/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/1d62240feff3/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/18505fe2bdb1/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/3f254c5ced1d/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/f4d5237a84f6/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/ce5d418183c5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/ce5d418183c5/kallisto_indexes.loc' for tool data table 'kallisto_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kallisto_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/4f9c4e6566e5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/4f9c4e6566e5/kallisto_indexes.loc' for tool data table 'kallisto_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'kallisto_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/stringtie/cbf488da3b2c/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f9d49f5cb597/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f9d49f5cb597/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/32dc5f781059/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/c370440f901e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/970e6333f07e/sam_fa_indices.loc' for tool data table 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'sam_fa_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/541082d03bef/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/26b4f9f98aca/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/b61f5d6a7f25/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/0e60e2dd20af/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/c9944a2600f1/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/a896b8b7d264/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/971e07ca4456/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,614 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/791f73caa0c8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,614 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/9473cd297a76/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,614 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/9473cd297a76/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/8aa352093d73/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/7b4454382d39/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/dd72ff87cfd0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/cfd81f17580b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/271965b55437/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/2c80b0d6bde0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/8b260d252ff4/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/ccb83bf54de0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/a730269af659/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/dadbd61dc4cf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0a5dcc9a8ec2/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/8f5962c43868/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/05f317e50e61/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/012656fd329f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bc5332d47b1c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/2331ddcbd5aa/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/591cc8518033/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/a12844ca467a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/b10d1510fa84/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/39bca000353d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/5b006286a458/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/fa65af07ce7d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/07396b423218/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/1a2ef636f48e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/46fcafba49ec/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/d237eaef451f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/2c372041ed8c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/283911fe7e1a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/31a1b89eab9b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/3897eaadfbff/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,622 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/5dc33613c288/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/3a72fede57ce/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/fcbeda41d0ac/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/abbc8041e8ec/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,623 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta_dbkeys.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,626 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,628 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,629 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/alignseq.loc' for 'alignseq_seq' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'alignseq_seq' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'twobit' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,632 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,634 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/tophat2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded 59 lines from '/cvmfs/data.galaxyproject.org/managed/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,636 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,637 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ce9', 'ce9', 'C. elegans (WS210): ce9', '/cvmfs/data.galaxyproject.org/managed/hisat2_index/ce9/ce9']) to data table 'hisat2_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded 47 lines from '/cvmfs/data.galaxyproject.org/managed/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,638 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,638 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['papHam1', 'papHam1', 'Baboon (Papio anubis): papHam1', '/cvmfs/data.galaxyproject.org/managed/bwa_mem_index/papHam1/papHam1.fa']) to data table 'bwa_mem_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded 20 lines from '/cvmfs/data.galaxyproject.org/managed/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,640 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,641 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken_databases.loc' for 'kraken_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1193 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys_ucsc.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,647 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded 14 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc' for 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,694 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/plant_tribes_scaffolds.loc' for 'plant_tribes_scaffolds' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,697 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plant_tribes_scaffolds' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/maf_indexes.loc' for 'maf_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'maf_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded 15 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,699 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken2_databases.loc' for 'kraken2_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken2_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded 237 lines from '/cvmfs/data.galaxyproject.org/byhand/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,703 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,706 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ornAna1', 'ornAna1', 'Platypus (Ornithorhynchus anatinus): ornAna1', '/cvmfs/data.galaxyproject.org/byhand/ornAna1/seq/ornAna1.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,708 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,708 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bfast_indexes.loc' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bfast_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb.loc' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,710 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb_p.loc' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_p' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,712 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,712 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded 16 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,714 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,717 [pN:job_handler_0,p:8,tN:MainThread] Loaded 201 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index.loc' for 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,717 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index_color.loc' for 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,720 [pN:job_handler_0,p:8,tN:MainThread] Loaded 24 lines from '/cvmfs/data.galaxyproject.org/byhand/location/maf_index.loc' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,720 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'indexed_maf_files' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ngs_sim_fasta.loc' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,721 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ngs_sim_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,723 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_base_index.loc' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,723 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_base_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,724 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_color_index.loc' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,724 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_color_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,725 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,726 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,729 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,729 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,729 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/cvmfs/data.galaxyproject.org/byhand/location/gatk_annotations.txt' for tool data table 'gatk_annotations' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,729 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_annotations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,731 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,731 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'srma_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,734 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'tophat_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,734 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'tophat_indexes_color' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,738 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,738 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,741 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ccat_configurations.loc' for 'ccat_configurations' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,741 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ccat_configurations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,742 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mosaik_index.loc' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,742 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mosaik_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,744 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'bowtie_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,744 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,746 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'bowtie_indexes_color' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,746 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,748 [pN:job_handler_0,p:8,tN:MainThread] Loaded 192 lines from '/cvmfs/data.galaxyproject.org/byhand/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,748 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,752 [pN:job_handler_0,p:8,tN:MainThread] Loaded 180 lines from '/cvmfs/data.galaxyproject.org/byhand/location/sam_fa_indices.loc' for 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,752 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'sam_fa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,756 [pN:job_handler_0,p:8,tN:MainThread] Loaded 177 lines from '/cvmfs/data.galaxyproject.org/byhand/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,756 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,762 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1181 lines from '/cvmfs/data.galaxyproject.org/byhand/location/liftOver.loc' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,762 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'liftOver' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,763 [pN:job_handler_0,p:8,tN:MainThread] Loaded 25 lines from '/cvmfs/data.galaxyproject.org/byhand/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,763 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,765 [pN:job_handler_0,p:8,tN:MainThread] Loaded 106 lines from '/cvmfs/data.galaxyproject.org/byhand/location/customProDB.loc' for 'customProDB' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,765 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'customProDB' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,766 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,766 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,767 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,767 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,768 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/snpeffv_genomedb.loc' for 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,768 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,769 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwameth_indexes.loc' for 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,769 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwameth_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,769 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/metaphlan_database_versioned.loc' for 'metaphlan_database_versioned' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,770 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'metaphlan_database_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,770 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/busco_database.loc' for 'busco_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,770 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'busco_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_config.tsv' for 'ncbi_fcs_gx_config' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,771 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_config' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_databases.loc' for 'ncbi_fcs_gx_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,772 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded 63 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_divisions.tsv' for 'ncbi_fcs_gx_divisions' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,773 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_divisions' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded 8 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rRNA_databases.loc' for 'rRNA_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,774 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rRNA_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mitos.loc' for 'mitos' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mitos' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_species.loc' for 'dada2_species' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_species' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_taxonomy.loc' for 'dada2_taxonomy' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mapseq_db.loc' for 'mapseq_db' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mapseq_db' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bracken_databases.loc' for 'bracken_databases' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bracken_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/plasmidfinder_database.loc' for 'plasmidfinder_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plasmidfinder_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus.loc' for 'amrfinderplus_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus_versioned.loc' for 'amrfinderplus_versioned_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_versioned_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bakta_database.loc' for 'bakta_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bakta_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,783 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/humann_protein_database.loc' for 'humann_protein_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'humann_protein_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/humann_nucleotide_database.loc' for 'humann_nucleotide_database' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'humann_nucleotide_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-10-05 06:23:01,796 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/all_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/all_fasta.loc.sample' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,797 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,797 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bfast_indexes.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,798 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bfast_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,798 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bfast_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,799 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb.loc.sample' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,800 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,800 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,800 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_p.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_p.loc.sample' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,801 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb_p' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,801 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb_p", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,801 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_d.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_d.loc.sample' for 'blastdb_d' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_d' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,803 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,803 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,803 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,804 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,804 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes_color' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,804 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes_color", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,804 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/maf_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/maf_index.loc.sample' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,806 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'indexed_maf_files' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,807 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,808 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ngs_sim_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,808 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "ngs_sim_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,808 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_base_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,809 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_base_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,810 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_base_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,810 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_color_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,811 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_color_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,811 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_color_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,812 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,812 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,812 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "picard_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,813 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,814 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,814 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'srma_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,814 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "srma_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,815 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/mosaik_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,816 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'mosaik_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,816 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "mosaik_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,817 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/twobit.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/twobit.loc.sample' for 'twobit' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,818 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,818 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "twobit", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +charset_normalizer DEBUG 2024-10-05 06:23:01,939 [pN:job_handler_0,p:8,tN:MainThread] Encoding detection: utf_8 is most likely the one. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,939 [pN:job_handler_0,p:8,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-lhaksg5j". +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,944 [pN:job_handler_0,p:8,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): + +galaxy.tool_util.data WARNING 2024-10-05 06:23:01,944 [pN:job_handler_0,p:8,tN:MainThread] Line 2 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): +AccessDeniedAccess DeniedHSYC51RXA9WE6V7T2D2bi4nkLeTHpMOKq5hhSLb4X8CrQ+Fdim7bqR5zivmqCUVr9S3iJv1FCO8GYSbU9djdm5JEhW4JkWkpxPGDSJB3da7DVsWZVyWuq32pbMM= +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-lhaksg5j' for 'igv_broad_genomes' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'igv_broad_genomes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-10-05 06:23:01,945 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/liftOver.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/liftOver.loc.sample' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,946 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'liftOver' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,946 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "liftOver", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,948 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bam_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/bam_iobio.loc.sample' for 'bam_iobio' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bam_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-10-05 06:23:01,949 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/vcf_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'vcf_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-10-05 06:23:01,950 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/biom_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'biom_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-10-05 06:23:01,951 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/intermine_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'intermine_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-10-05 06:23:01,952 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/icn3d_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'icn3d_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,953 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,954 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,954 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,954 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,954 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,954 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,954 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,955 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,955 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,955 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,955 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,955 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,955 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,956 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,956 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,956 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,956 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,956 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-10-05 06:23:01,957 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/q2view_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/q2view_display.loc.sample' for 'q2view_display' +galaxy.tool_util.data DEBUG 2024-10-05 06:23:01,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'q2view_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.managers.dbkeys ERROR 2024-10-05 06:23:01,958 [pN:job_handler_0,p:8,tN:MainThread] ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy/server/database/tool-data/\n/cvmfs/data.galaxyproject.org/managed/location/builds.txt' +galaxy.util WARNING 2024-10-05 06:23:03,874 [pN:job_handler_0,p:8,tN:MainThread] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-10-05 06:23:03,876 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:23:03,876 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:03,877 [pN:job_handler_0,p:8,tN:MainThread] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:23:03,927 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:23:03,928 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:23:04,117 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:23:04,117 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:23:04,120 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-10-05 06:23:04,166 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:23:04,166 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:04,191 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,196 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_trim' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,204 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_removereads' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,209 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff_sars_cov_2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,222 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_filtervariants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,233 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_getmasked' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,238 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_variants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,244 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_trim' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,253 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_removereads' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,258 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,265 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_filtervariants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,269 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_variants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,277 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,287 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_gtcheck' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,297 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fixploidy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,308 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_to_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,322 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_norm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,340 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query_list_samples' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,347 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_missing2ref' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,357 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_cnv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,371 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_setgt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,382 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_counts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,392 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_mpileup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,412 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_mendelian' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,423 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_concat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,432 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_from_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,450 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_impute_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,461 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_reheader' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,471 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,488 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_an_ac' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,498 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_tags' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,509 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_isec' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,523 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,534 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_roh' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,551 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,581 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,604 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,620 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_csq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,635 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,650 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_dosage' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,661 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,673 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_tag2tag' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,686 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcf2tsv' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,690 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfaddinfo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,695 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,700 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotategenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,708 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbedintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,713 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbreakcreatemulti' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,718 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcheck' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,724 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcombine' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,729 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcommonsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffixup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,739 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfflatten' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,743 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgeno2haplo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,749 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,753 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfhethom' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,757 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfleftalign' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,763 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfprimers' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,767 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfrandomsample' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,773 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfsort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,777 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfvcfintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,783 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfselectsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,788 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,792 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffilter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,798 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,803 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_annotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,806 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_slice' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,809 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,815 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,830 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_gtcheck' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,840 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fixploidy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,852 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_to_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,865 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_norm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,884 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query_list_samples' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,891 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_missing2ref' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,903 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_cnv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,920 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_setgt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,932 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_counts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,943 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_mpileup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,964 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_mendelian' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,978 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_concat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:04,990 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_from_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,007 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_impute_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,019 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_reheader' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,027 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_an_ac' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,057 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_tags' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,072 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_isec' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,086 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,098 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_roh' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,114 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,138 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,157 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,174 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_csq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,191 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,206 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_dosage' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,218 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,231 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_tag2tag' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,243 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,479 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,713 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,948 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collapse_collections' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_to_collection' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,964 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pick_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,974 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_to_collection' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,990 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_element_identifiers' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,993 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_column_join' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:05,997 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_matrix' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,011 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_heatmap' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,028 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,041 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_pe_fragmentsize' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,052 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bigwig_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,062 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,072 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_correct_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,083 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bam_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,096 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bigwig_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_correlation' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,121 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,136 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_enrichment' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,150 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_fingerprint' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,164 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_pca' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,173 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,186 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_profile' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,197 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_matrix' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,211 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_heatmap' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,244 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_pe_fragmentsize' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,254 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bigwig_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,265 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,276 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_correct_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,285 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bam_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,299 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bigwig_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,310 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_correlation' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,325 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,340 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_enrichment' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,354 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_fingerprint' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,368 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_pca' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,379 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,394 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_profile' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,408 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,436 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,451 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,457 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trimmomatic' from owner 'pjbriggs' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,468 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,504 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,508 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,527 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,563 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,583 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,602 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,619 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,623 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,690 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,708 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,732 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ncbi_acc_download' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,740 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,767 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,796 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ncbi_acc_download' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,805 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pygenometracks' from owner 'iuc' was not found in database. Tool will be loaded without install database. +:1: SyntaxWarning: invalid escape sequence '\d' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:06,881 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'circos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,005 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-10-05 06:23:07,048 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,061 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,066 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-10-05 06:23:07,111 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,125 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,136 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,145 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,153 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,159 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,166 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,171 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'minimap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,184 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bowtie2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,218 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,264 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwameth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,269 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lastz' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,291 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,319 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,350 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,369 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,395 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,437 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'minimap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,453 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bowtie2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,484 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,528 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwameth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,534 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lastz' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,556 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,599 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,642 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,690 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,741 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_nucmer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,752 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummerplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,760 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_show_coords' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_dnadiff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,773 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,783 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_delta_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,789 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_nucmer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,801 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummerplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_show_coords' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,816 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_dnadiff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,823 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,833 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_delta_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,840 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,848 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,854 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,861 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,871 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,878 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'nanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,887 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_events' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,892 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_hist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,897 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_occupancy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,902 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualpos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,907 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_squiggle' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,914 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_yield_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,919 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'porechop' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,926 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_winner' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,931 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_times' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,936 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,942 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,948 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,952 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_nucdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,958 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,963 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,971 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,981 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:07,989 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,000 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'nanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,020 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'porechop' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,026 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:08,039 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fa', which is used in the 'format' attribute of parameter 'transcript' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_pseudo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,052 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_quant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,060 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,080 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'edger' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,089 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sailfish' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,096 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,118 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'stringtie' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,137 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,148 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,156 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,481 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,505 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,519 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,536 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,543 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cufflinks' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,552 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deg_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,557 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,565 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,574 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,590 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,600 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'egsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,608 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fgsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:08,633 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fa', which is used in the 'format' attribute of parameter 'transcript' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,640 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_pseudo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,650 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_quant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,660 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,675 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,690 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'edger' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'stringtie' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,723 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,735 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'brew3r_r' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,741 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:08,872 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,005 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pileup_interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,016 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,035 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_reheader' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,040 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_pileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,052 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,056 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam2interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,059 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_multi_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,066 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,074 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,081 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,087 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fixmate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,093 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fastx' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,108 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_depth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,115 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,130 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,136 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_bedcov' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,141 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_calmd' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,151 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,158 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtool_filter2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,165 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_flagstat' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,171 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_sort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,180 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_mpileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,195 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bam_to_sam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,202 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,216 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_to_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,225 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_slice_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,233 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_rmdup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,239 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_on_md' from owner 'boris' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,242 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_merge' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,245 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,253 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,260 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,266 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,273 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,278 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,288 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,308 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,328 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,334 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'revertr2orientationinbam' from owner 'lldelisle' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,336 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,345 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,365 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,386 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_reheader' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,391 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,398 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,402 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_multi_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,409 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,415 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,422 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fixmate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,428 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fastx' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,444 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_depth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,452 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,464 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,469 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_bedcov' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,476 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_calmd' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,483 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,488 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_flagstat' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_sort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,499 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_mpileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,510 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bam_to_sam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,515 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,525 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_to_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,531 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_slice_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,538 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,547 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,564 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,567 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sqlite_to_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,573 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,577 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'concatenate_multiple_datasets' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,579 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'regex_find_replace' from owner 'galaxyp' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,586 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_on_column' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,615 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'add_input_name_as_column' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,618 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_melt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,708 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_cast' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,712 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,716 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gff3_rebase' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,721 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_remove_by_header' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,725 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_order_header_sort' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,728 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'replace_column_by_key_value_file' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,731 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,816 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,836 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,841 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,847 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,873 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,960 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,965 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:09,969 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,066 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,072 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,082 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,101 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,108 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sqlite_to_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,115 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,121 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'regex_find_replace' from owner 'galaxyp' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,130 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_on_column' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,338 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_remove_by_header' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,341 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,352 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_viterbi' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,358 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_indelqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,365 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,376 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_alnqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,382 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,407 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_genesets' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,412 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_dbnsfp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,419 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,454 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,496 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,502 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sniffles' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,509 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jasminesv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,524 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,535 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,546 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,569 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,588 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,624 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,644 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_indelqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,649 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_alnqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,655 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,690 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'diff' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,695 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'unicycler' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,707 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'spades' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,717 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'miniasm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,722 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'racon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,729 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'unicycler' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,739 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'miniasm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,744 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'racon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,753 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gfastats' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-10-05 06:23:10,761 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0': a when tag has been defined for 'target_condition (target_option) --> false', but does not appear to be selectable. +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:10,761 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'text', which is used in the 'format' attribute of parameter 'swiss_army_knife' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,791 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pharmcat' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,798 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pharmcat' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,806 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name '10x_bamtofastq' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,820 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,838 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'chromeister' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,843 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,854 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,860 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,869 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:10,873 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0': a when tag has not been defined for 'add_metadata (add_metadata_file) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,875 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_empty_drops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,880 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,901 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,912 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,925 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,937 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,966 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmonquantmerge' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,972 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'slice_image' from owner 'imgteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,975 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_tsne' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,984 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,988 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,992 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:10,997 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_exprs_freq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,002 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,006 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,031 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,048 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,078 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,093 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-10-05 06:23:11,386 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,423 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,435 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_parameter_iterator' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,442 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'droplet_barcode_plot' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,446 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,453 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtf2gene_list' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,458 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,461 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sceasy_convert' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,469 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:11,475 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,477 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'retrieve_scxa' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,481 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_inspect_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:11,484 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'rdata.eset', which is used in the 'format' attribute of parameter 'rds_eset' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,485 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_construct_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,511 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,524 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,534 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,547 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,560 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,568 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,574 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,579 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,584 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-10-05 06:23:11,882 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,919 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,926 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,929 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:11,935 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,937 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,955 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,963 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,972 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:11,977 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+3+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:11,985 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.6.0+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,988 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:11,996 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,004 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,011 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,018 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,027 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,035 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,043 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,051 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,059 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,067 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,074 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,082 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,090 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,098 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,108 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,117 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,126 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,134 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,145 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,154 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,164 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,472 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,481 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,488 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,497 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,510 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,553 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,561 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_groomer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,569 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_manipulation' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,579 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fasta_compute_length' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,582 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_deinterlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,587 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_interlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,593 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flash' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,600 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trim_galore' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,610 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,619 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,631 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,640 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,649 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,710 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,726 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,740 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'seq_filter_by_id' from owner 'peterjc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,745 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,805 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,827 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,834 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,838 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,861 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,864 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,864 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_2' +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,868 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,884 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,912 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,914 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,915 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_2' +galaxy.tools.parameters.basic WARNING 2024-10-05 06:23:12,920 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fasta.bz2', which is used in the 'format' attribute of parameter 'input_1' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,939 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trim_galore' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,954 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_reverse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,959 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,964 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_ops' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,971 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,976 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,981 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_reverse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,985 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,990 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_ops' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:12,998 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,178 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,353 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,523 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,720 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'map_param_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,728 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'compose_text_param' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,731 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'map_param_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,739 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtftobed12' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,743 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,751 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,757 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,764 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,769 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,802 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__export' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,832 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__import' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,873 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft_add' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,877 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,881 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mask' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,885 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__add_pseudocount' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,889 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancombc' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,893 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,896 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancom' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,900 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,906 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,912 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,923 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_pyro' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,927 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_ccs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,932 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,936 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,942 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_16s' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_other' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,950 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__visualize_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,953 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,957 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,960 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,963 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,967 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,971 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,975 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,979 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__adonis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,983 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__umap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,986 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,989 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__bioenv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,993 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa_biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:13,996 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__tsne' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,000 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,005 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__procrustes_analysis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__mantel' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,014 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,019 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,023 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,032 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,038 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,042 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__filter_distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,049 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,053 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,057 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,061 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,066 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__observed_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__bray_curtis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,073 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,077 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__alpha_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,080 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__shannon_entropy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,084 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__jaccard' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,088 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__pielou_evenness' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,091 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_meta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,095 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__weighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,103 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__unweighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,109 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,116 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__faith_pd' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,122 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__procrustes_plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,128 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,132 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,138 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,143 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,147 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_naive_bayes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,153 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,158 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__extract_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,162 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_hybrid_vsearch_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,169 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_vsearch' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,175 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,179 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__find_consensus_annotation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,183 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__vsearch_global' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,188 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,191 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__presence_absence' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,194 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,199 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,203 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features_conditionally' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,206 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rename_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,212 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,215 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__relative_frequency' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,219 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,222 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,227 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rarefy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,231 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__transpose' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,235 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__subsample' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,239 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,246 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,250 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__core_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,254 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__group' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,258 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,262 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__sepp' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,266 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__classify_otus_experimental' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,270 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,273 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,278 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__correlation_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,282 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__dendrogram_heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,287 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__gradient_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,292 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_ordination' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,296 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__assign_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,300 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_differential' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,304 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_hierarchical' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,309 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,315 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,321 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__nmit' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,326 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,331 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__plot_feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,336 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,340 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__linear_mixed_effects' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,705 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,711 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,717 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__anova' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,721 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__maturity_index' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,730 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__shuffle_groups' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,738 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,741 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml_rapid_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,745 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,748 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,755 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,763 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__robinson_foulds' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,771 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,774 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__midpoint_root' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,777 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,782 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,785 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_tree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,790 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree_ultrafast_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,797 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_composition' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,802 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,806 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__filter_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__bowtie2_build' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,814 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,819 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__exclude_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,824 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_filter__q_score' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__metatable' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,833 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_classifier' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,837 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,844 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,850 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__scatterplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,853 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_from_dist' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,858 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__confusion_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,863 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__split_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,868 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,871 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,880 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,885 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_regressor' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,889 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_classification' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,893 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,898 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_regression' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,902 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__collapse' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,906 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,912 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__barplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,918 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,924 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_closed_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,930 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_open_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,936 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__merge_pairs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,941 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_denovo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__dereplicate_sequences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__fastq_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,956 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_ref' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,962 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_de_novo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:14,967 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,046 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,121 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,203 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,259 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,262 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,265 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,314 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,369 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_regression_performance_plots' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,372 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pygenometracks' from owner 'iuc' was not found in database. Tool will be loaded without install database. +:1: SyntaxWarning: invalid escape sequence '\d' +:1: SyntaxWarning: invalid escape sequence '\d' +:1: SyntaxWarning: invalid escape sequence '\d' +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,459 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'circos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,573 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,578 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,585 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,594 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,601 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,612 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'chromeister' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,617 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,628 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,635 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,663 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,677 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,693 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,717 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmonquantmerge' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,741 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,765 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,783 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,811 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:15,827 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,205 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,218 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,224 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtf2gene_list' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,229 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:16,238 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,241 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_parameter_iterator' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,247 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,266 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:16,273 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.9.3+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,276 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,286 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,294 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,302 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,312 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,322 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,332 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,340 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,351 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-10-05 06:23:16,359 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cite_seq_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,370 [pN:job_handler_0,p:8,tN:MainThread] Reading tools from config files finished (12494.889 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,371 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,371 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,371 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,372 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,373 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,374 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,375 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,376 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,377 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,378 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,379 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,380 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,381 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,382 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,383 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,384 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,385 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,386 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,387 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,388 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,390 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,391 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,392 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,393 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,394 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,395 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,396 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,397 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,398 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,399 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,401 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,402 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,403 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,404 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,405 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,406 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,407 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,409 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,410 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,411 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,412 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,413 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,414 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,415 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,416 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,417 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,419 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,420 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,421 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,422 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,423 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,424 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,425 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,429 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,430 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,431 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,432 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,433 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,434 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,435 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,436 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,437 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,438 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,439 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,440 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,441 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,442 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,443 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,444 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,445 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,446 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,447 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1, version: 0.0.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0, version: 0.0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,448 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,455 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 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[pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,456 [pN:job_handler_0,p:8,tN:MainThread] Loading section: GEMINI +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,456 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_paired/qiime2__cutadapt__trim_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,457 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_single/qiime2__cutadapt__demux_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_paired/qiime2__cutadapt__demux_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_pyro/qiime2__dada2__denoise_pyro/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_ccs/qiime2__dada2__denoise_ccs/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__denoise_16s/qiime2__deblur__denoise_16S/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__denoise_other/qiime2__deblur__denoise_other/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__deblur__visualize_stats/qiime2__deblur__visualize_stats/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__subsample_paired/qiime2__demux__subsample_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__subsample_single/qiime2__demux__subsample_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,458 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__filter_samples/qiime2__demux__filter_samples/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_correlation/qiime2__diversity__beta_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__adonis/qiime2__diversity__adonis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__umap/qiime2__diversity__umap/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,459 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,460 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,471 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 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toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,479 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,480 [pN:job_handler_0,p:8,tN:MainThread] Loading tool panel finished (108.957 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,486 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,487 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,488 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,489 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,490 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,491 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,492 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,493 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,494 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,495 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,496 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,497 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,498 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,499 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,500 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,501 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,502 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,503 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,504 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,505 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,506 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,507 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,508 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,509 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,510 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,511 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,512 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,513 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,514 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,515 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,516 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,517 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,518 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,519 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,520 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,521 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,522 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,523 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,524 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,525 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,526 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,527 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,528 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,529 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,530 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,531 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,532 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,533 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,534 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,535 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,536 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,538 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,539 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,540 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,541 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,542 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,543 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,544 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,545 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,546 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,547 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,548 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,549 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,550 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,551 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,552 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,553 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,554 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,555 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,556 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,557 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,558 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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06:23:16,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,577 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_paired/qiime2__cutadapt__trim_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_single/qiime2__cutadapt__demux_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_paired/qiime2__cutadapt__demux_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_pyro/qiime2__dada2__denoise_pyro/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,578 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,611 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,611 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,617 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,618 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,621 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,622 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,623 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,632 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,635 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,639 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,640 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,643 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,644 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,645 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,647 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,648 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,649 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,650 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,651 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,652 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,653 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,654 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,655 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,656 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,657 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,658 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,659 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,660 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,661 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,662 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,663 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,664 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,665 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,666 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,667 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,668 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,669 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,670 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,671 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,672 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,673 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,674 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,675 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,676 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,677 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,678 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,680 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,685 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,686 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,687 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,689 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2, version: v0.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,694 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[pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,699 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool 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3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,702 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics/qiime2__diversity__core_metrics/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_correlation/qiime2__diversity__alpha_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__filter_distance_matrix/qiime2__diversity__filter_distance_matrix/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded 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panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,727 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,727 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,727 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,729 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:23:16,729 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-10-05 06:23:16,729 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (125.702 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2024-10-05 06:23:16,729 [pN:job_handler_0,p:8,tN:MainThread] Writing integrated tool panel config file to '/galaxy/server/config/mutable/integrated_tool_panel.xml' +galaxy.tool_util.deps WARNING 2024-10-05 06:23:16,741 [pN:job_handler_0,p:8,tN:MainThread] Path '/galaxy/server/database/deps' does not exist, ignoring +galaxy.tool_util.deps WARNING 2024-10-05 06:23:16,741 [pN:job_handler_0,p:8,tN:MainThread] Path '/galaxy/server/database/deps' is not directory, ignoring +galaxy.tool_util.deps.installable WARNING 2024-10-05 06:23:16,753 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.installable WARNING 2024-10-05 06:23:16,759 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.containers DEBUG 2024-10-05 06:23:16,765 [pN:job_handler_0,p:8,tN:MainThread] Loading container resolution config from file '/galaxy/server/config/container_resolvers_conf.xml' +galaxy.tools.search WARNING 2024-10-05 06:23:16,769 [pN:job_handler_0,p:8,tN:MainThread] Index at '/galaxy/server/database/tool_search_index/default' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2024-10-05 06:23:16,781 [pN:job_handler_0,p:8,tN:MainThread] Index at '/galaxy/server/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2024-10-05 06:23:16,792 [pN:job_handler_0,p:8,tN:MainThread] Index at '/galaxy/server/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,815 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,816 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,817 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,820 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,824 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,826 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,827 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,828 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,830 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'minerva_tabular' for datatype 'tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,838 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,839 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,840 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,840 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,840 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,841 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,842 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a3m' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,843 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,845 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,845 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,845 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,845 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,845 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,846 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,848 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,882 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,885 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,886 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,888 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,889 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,890 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,891 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,894 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,895 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,897 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,899 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,901 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,903 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,905 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,907 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,908 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,909 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,912 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,913 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,914 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,915 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,917 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,918 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,921 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,966 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,970 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,973 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,976 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,977 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,979 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,981 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,986 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,989 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,992 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,993 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,995 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,997 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:16,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,005 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,006 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,008 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,009 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,011 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,012 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,013 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,014 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,016 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,017 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,018 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,019 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,021 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,022 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,023 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,024 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,025 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,027 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,028 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,030 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,033 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,036 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,039 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,041 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,042 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,044 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,046 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,048 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,050 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,052 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,054 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,056 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,059 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,060 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,063 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,065 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,067 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,069 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,071 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,073 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,075 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,077 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,079 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,081 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,082 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,084 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,085 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,088 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,090 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,092 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,093 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,094 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,096 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,097 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,098 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,100 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,101 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,102 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,103 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,104 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-10-05 06:23:17,106 [pN:job_handler_0,p:8,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:23:17,108 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:23:17,109 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:23:17,112 [pN:job_handler_0,p:8,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:23:17,113 [pN:job_handler_0,p:8,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,115 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,116 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,117 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,117 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,118 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,119 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,119 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,120 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,121 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,121 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,122 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,123 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,123 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,123 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,124 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,124 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,127 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,130 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,131 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,132 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,132 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,132 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,135 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,138 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,140 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,143 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,145 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,146 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,146 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,146 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,147 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,147 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,148 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,148 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,149 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,150 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,154 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,156 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,160 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,162 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,165 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,168 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,172 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,174 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,176 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,180 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,183 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,186 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,190 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,190 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,191 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,192 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,193 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,194 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,195 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: tiffviewer +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,196 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,197 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.config_parser INFO 2024-10-05 06:23:17,198 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,198 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2024-10-05 06:23:17,199 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2024-10-05 06:23:17,218 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2024-10-05 06:23:17,228 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.windows' +galaxy.tours._impl INFO 2024-10-05 06:23:17,239 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2024-10-05 06:23:17,257 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2024-10-05 06:23:17,263 [pN:job_handler_0,p:8,tN:MainThread] Initializing job handler +galaxy.jobs INFO 2024-10-05 06:23:17,263 [pN:job_handler_0,p:8,tN:MainThread] Handler 'job_handler_0' will load all configured runner plugins +galaxy.jobs.runners DEBUG 2024-10-05 06:23:17,265 [pN:job_handler_0,p:8,tN:MainThread] Loading KubernetesRunner with params: {'k8s_cleanup_job': 'onsuccess', 'k8s_data_volume_claim': 'edge-24-10-05-06-10-1-galaxy-galaxy-pvc:/galaxy/server/database', 'k8s_fs_group_id': '101', 'k8s_galaxy_instance_id': 'edge-24-10-05-06-10-1-galaxy', 'k8s_interactivetools_ingress_annotations': '\nnginx.ingress.kubernetes.io/auth-tls-pass-certificate-to-upstream: "true"\nnginx.ingress.kubernetes.io/auth-tls-secret: \'edge-24-10-05-06-10-1/ca-secret\'\nnginx.ingress.kubernetes.io/auth-tls-verify-client: "on"\nnginx.ingress.kubernetes.io/auth-tls-verify-depth: "1"\nnginx.ingress.kubernetes.io/proxy-body-size: 10G\nnginx.ingress.kubernetes.io/proxy-read-timeout: "600"\nnginx.ingress.kubernetes.io/ssl-redirect: "true"\n', 'k8s_interactivetools_use_ssl': True, 'k8s_job_ttl_secs_after_finished': 90, 'k8s_namespace': 'edge-24-10-05-06-10-1', 'k8s_node_selector': 'cloud.google.com/gke-nodepool: default-pool', 'k8s_persistent_volume_claims': 'edge-24-10-05-06-10-1-galaxy-galaxy-pvc/config:/galaxy/server/database/config:r,edge-24-10-05-06-10-1-galaxy-galaxy-pvc/tmp:/galaxy/server/database/tmp:rw,edge-24-10-05-06-10-1-galaxy-galaxy-pvc/tool-data:/galaxy/server/database/tool-data:rw,edge-24-10-05-06-10-1-galaxy-galaxy-pvc/tools:/galaxy/server/database/tools:r,edge-24-10-05-06-10-1-galaxy-galaxy-pvc/shed_tools:/galaxy/server/database/shed_tools:r,edge-24-10-05-06-10-1-galaxy-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:r,edge-24-10-05-06-10-1-galaxy-galaxy-pvc/cvmfsclone:/cvmfs/cloud.galaxyproject.org:r', 'k8s_pod_priority_class': 'edge-24-10-05-06-10-1-priority-class', 'k8s_pull_policy': 'IfNotPresent', 'k8s_supplemental_group_id': '101', 'k8s_use_service_account': True, 'k8s_working_volume_claim': 'edge-24-10-05-06-10-1-galaxy-galaxy-pvc:/galaxy/server/database'} +galaxy.jobs.runners.state_handler_factory DEBUG 2024-10-05 06:23:17,266 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners.util.pykube_util ERROR 2024-10-05 06:23:17,267 [pN:job_handler_0,p:8,tN:MainThread] Galaxy instance [edge-24-10-05-06-10-1-galaxy] is either too long (>20 characters) or it includes non DNS acceptable characters, ignoring it. +galaxy.jobs DEBUG 2024-10-05 06:23:17,267 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.kubernetes:KubernetesJobRunner' as 'k8s' +galaxy.jobs.runners.state_handler_factory DEBUG 2024-10-05 06:23:17,268 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2024-10-05 06:23:17,268 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.handler DEBUG 2024-10-05 06:23:17,269 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runners plugins: k8s:local +galaxy.jobs.runners DEBUG 2024-10-05 06:23:17,281 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 KubernetesRunner workers +galaxy.jobs.runners DEBUG 2024-10-05 06:23:17,282 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2024-10-05 06:23:17,283 [pN:job_handler_0,p:8,tN:MainThread] Handler queue starting for jobs assigned to handler: job_handler_0 +galaxy.jobs.handler INFO 2024-10-05 06:23:17,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'db-skip-locked' assignment method for handler 'job_handler_0', tag(s): _default_ +galaxy.jobs.handler INFO 2024-10-05 06:23:17,297 [pN:job_handler_0,p:8,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2024-10-05 06:23:17,298 [pN:job_handler_0,p:8,tN:MainThread] job handler stop queue started +galaxy.web_stack.handlers DEBUG 2024-10-05 06:23:17,302 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-10-05 06:23:17,302 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-10-05 06:23:17,302 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.web_stack.handlers INFO 2024-10-05 06:23:17,322 [pN:job_handler_0,p:8,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on to override the default +galaxy.workflow.scheduling_manager INFO 2024-10-05 06:23:17,322 [pN:job_handler_0,p:8,tN:MainThread] Workflow scheduling handler assignment method(s): db-skip-locked +galaxy.workflow.scheduling_manager INFO 2024-10-05 06:23:17,322 [pN:job_handler_0,p:8,tN:MainThread] Tag [schedulers] handlers: workflow_scheduler0 +galaxy.web_stack.handlers DEBUG 2024-10-05 06:23:17,322 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.queue_worker INFO 2024-10-05 06:23:17,328 [pN:job_handler_0,p:8,tN:MainThread] Binding and starting galaxy control worker for job_handler_0 +galaxy.queue_worker INFO 2024-10-05 06:23:17,329 [pN:job_handler_0,p:8,tN:MainThread] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.model.database_heartbeat DEBUG 2024-10-05 06:23:17,356 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is config watcher +galaxy.app INFO 2024-10-05 06:23:17,371 [pN:job_handler_0,p:8,tN:MainThread] Galaxy app startup finished (17778.723 ms) +galaxy.web_stack INFO 2024-10-05 06:23:17,371 [pN:job_handler_0,p:8,tN:MainThread] Galaxy server instance 'job_handler_0' is running +galaxy.queue_worker INFO 2024-10-05 06:23:17,379 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:23:17,379 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.model.database_heartbeat DEBUG 2024-10-05 06:24:17,366 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is not config watcher +galaxy.queue_worker INFO 2024-10-05 06:24:24,721 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:24:24,721 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-10-05 06:24:24,762 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-10-05 06:24:24,770 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:24:24,770 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,770 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:24:24,773 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:24:24,773 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:24:24,775 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:24:24,775 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:24:24,777 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-10-05 06:24:24,779 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:24:24,780 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,800 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tools WARNING 2024-10-05 06:24:24,840 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (71.945 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,843 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,853 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,855 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,856 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,857 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,861 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,862 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,863 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,864 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,866 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,867 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,868 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,869 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,870 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,871 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,872 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,873 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,874 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,874 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,874 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,874 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,874 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,874 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,875 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,876 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,877 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,878 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,879 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,880 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,886 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,887 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,888 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,889 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,890 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,905 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,912 [pN:job_handler_0,p:8,tN:Thread-1] 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1, version: 0.0.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0, version: 0.0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2, version: v0.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,918 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics/qiime2__diversity__core_metrics/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_correlation/qiime2__diversity__alpha_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,949 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (107.910 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,959 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,960 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,961 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,962 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,963 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,964 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,965 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,966 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,967 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,968 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,969 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,970 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,971 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,972 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,974 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,975 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:24,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,018 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,019 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,020 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-10-05 06:24:25,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,091 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into 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06:24:25,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1, version: 0.0.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0, version: 0.0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2, version: v0.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0, version: 0.1.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1, version: 1.6.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,166 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,166 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,166 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.6.0+galaxy0, version: 1.6.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,166 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+3+galaxy0, version: 1.8.1+3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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DEBUG 2024-10-05 06:24:25,171 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,171 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,171 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,172 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,177 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,177 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,177 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,198 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:24:25,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-10-05 06:24:25,198 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (126.254 ms) +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-10-05 06:24:25,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:24:25,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:24:25,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:24:25,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:24:25,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-10-05 06:24:25,219 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-10-05 06:24:25,220 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (499.032 ms) +galaxy.queue_worker INFO 2024-10-05 06:24:25,221 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:24:25,221 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.jobs.handler DEBUG 2024-10-05 06:25:49,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 1 +tpv.rules.gateway INFO 2024-10-05 06:25:49,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] loading tpv rules from: ['https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml', 'lib/galaxy/jobs/rules/tpv_rules_local.yml', 'https://gist.githubusercontent.com/afgane/68d1dbbe0af2468ba347dc74b6d3f7fa/raw/20edda50161bdcb74ff38935e7f76d79bfdaf303/tvp_rules_tests.yml'] +tpv.rules.gateway INFO 2024-10-05 06:25:49,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Watching for changes in file: lib/galaxy/jobs/rules/tpv_rules_local.yml +tpv.core.entities DEBUG 2024-10-05 06:25:49,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:25:49,923 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:25:49,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:25:49,961 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:25:50,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Working directory for job is: /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs.runners DEBUG 2024-10-05 06:25:50,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [1] queued (78.696 ms) +galaxy.jobs.handler INFO 2024-10-05 06:25:50,021 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:25:50,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 1 +galaxy.jobs DEBUG 2024-10-05 06:25:50,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [1] prepared (160.399 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:25:50,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/1/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/1/registry.xml' '/galaxy/server/database/jobs_directory/000/1/upload_params.json' '1:/galaxy/server/database/objects/7/d/b/dataset_7dbb9727-7b58-466d-9655-008e23538f17_files:/galaxy/server/database/objects/7/d/b/dataset_7dbb9727-7b58-466d-9655-008e23538f17.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:25:50,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (1) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/1/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/1/galaxy_1.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:25:50,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 1 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:25:50,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 1 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:25:51,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:05,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tvn2x with k8s id: gxy-tvn2x succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:26:05,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 1: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:26:15,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 1 finished +galaxy.model.metadata DEBUG 2024-10-05 06:26:15,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1 +galaxy.jobs INFO 2024-10-05 06:26:15,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 1 in /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs DEBUG 2024-10-05 06:26:15,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 1 executed (115.165 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:15,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 1 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:26:15,495 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 2 +tpv.core.entities DEBUG 2024-10-05 06:26:15,533 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/.*, abstract=False, cores=1, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:26:15,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:26:15,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:26:15,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:26:15,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs.runners DEBUG 2024-10-05 06:26:15,577 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [2] queued (38.331 ms) +galaxy.jobs.handler INFO 2024-10-05 06:26:15,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:15,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 2 +galaxy.jobs DEBUG 2024-10-05 06:26:15,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [2] prepared (54.124 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:26:15,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:26:15,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1: datamash:1.8 +galaxy.tool_util.deps.mulled.util DEBUG 2024-10-05 06:26:15,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Querying https://quay.io/api/v1/repository for repos within biocontainers +galaxy.queue_worker INFO 2024-10-05 06:26:31,914 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:26:31,914 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-10-05 06:26:31,962 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-10-05 06:26:31,969 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:31,969 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:31,970 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:31,971 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:31,971 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:31,973 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:31,973 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:31,975 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-10-05 06:26:31,978 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:31,978 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:31,999 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tools WARNING 2024-10-05 06:26:32,049 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:32,049 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (81.472 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,056 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,092 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,093 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,094 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,095 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,096 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,097 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,103 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,104 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,105 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,106 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,107 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,108 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,113 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,114 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,115 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,116 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,117 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,127 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,146 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1, version: 3.3.2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: EMBOSS +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,156 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357, version: 357 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: GEMINI +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1, version: 0.20.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2, version: 0.20.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2022.11.1+dist.h2bda5906.2, version: 2022.11.1+dist.h2bda5906.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__add_pseudocount/qiime2__composition__add_pseudocount/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancombc/qiime2__composition__ancombc/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__tabulate/qiime2__composition__tabulate/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__composition__ancom/qiime2__composition__ancom/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_single/qiime2__cutadapt__trim_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__trim_paired/qiime2__cutadapt__trim_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_single/qiime2__cutadapt__demux_single/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__cutadapt__demux_paired/qiime2__cutadapt__demux_paired/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_pyro/qiime2__dada2__denoise_pyro/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_ccs/qiime2__dada2__denoise_ccs/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2022.11.2+q2galaxy.2022.11.1.2, version: 2022.11.2+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,177 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,177 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,178 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,179 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,180 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,181 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (130.990 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,192 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,192 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,192 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,204 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,205 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,207 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,208 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,209 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,210 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,211 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,213 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,215 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,216 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,217 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,220 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,221 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,222 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,223 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,224 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,225 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,226 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,227 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,228 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,229 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,230 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,230 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,230 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,231 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,231 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,231 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,231 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,231 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,232 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,233 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,234 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,235 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,236 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,237 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,238 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,239 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,240 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,241 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,242 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,243 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,244 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,245 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,246 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,247 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,248 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,249 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,250 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,251 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,251 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,251 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,251 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,251 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,252 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,253 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,254 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,254 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,254 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,254 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,255 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,256 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,257 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,272 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,272 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,272 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,292 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,293 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,294 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,295 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,295 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-10-05 06:26:32,295 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (113.919 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,303 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,304 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,305 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,306 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,307 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,308 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,309 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,310 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,311 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,312 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,316 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,317 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,318 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,319 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,320 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,321 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,321 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,322 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,323 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,324 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,324 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,324 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,324 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,325 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,326 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,327 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,328 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,329 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,330 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,331 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,332 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,333 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,334 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,335 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,336 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,337 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,338 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,339 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,340 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,341 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,342 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,343 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,343 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,343 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,343 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,343 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,343 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,344 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,345 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,346 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,347 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,348 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,349 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,350 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,351 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,352 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,353 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,354 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,355 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,356 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,357 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,358 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,359 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,360 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,361 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,362 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,363 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,364 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,365 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,366 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,367 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,368 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,369 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,370 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,371 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,372 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,373 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,374 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,375 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,376 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,377 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,378 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,379 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,380 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,381 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,382 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,383 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,384 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,385 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,386 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,387 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,388 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,389 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,390 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,390 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,390 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,390 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,390 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,390 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,391 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,392 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,393 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,394 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,395 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,395 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,395 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,395 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,395 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,395 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,396 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,397 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,398 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,398 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,398 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,398 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,398 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,398 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,399 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,400 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,400 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,400 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,400 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,400 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,400 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,401 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,401 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,401 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,401 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,401 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,402 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,402 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,402 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,402 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,402 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,403 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,404 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,405 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,405 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,405 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,405 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,406 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 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DEBUG 2024-10-05 06:26:32,417 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,417 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,417 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,417 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,420 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-10-05 06:26:32,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,426 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,448 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:32,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-10-05 06:26:32,448 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (152.742 ms) +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:32,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:32,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:32,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:32,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:32,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-10-05 06:26:32,468 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-10-05 06:26:32,469 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (554.841 ms) +galaxy.queue_worker INFO 2024-10-05 06:26:32,470 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:26:32,470 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.queue_worker INFO 2024-10-05 06:26:36,643 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:26:36,643 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-10-05 06:26:36,670 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-10-05 06:26:36,679 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:36,679 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,680 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:36,680 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:36,680 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:36,683 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:36,683 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-10-05 06:26:36,685 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-10-05 06:26:36,689 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:36,689 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,714 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tools WARNING 2024-10-05 06:26:36,771 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:36,771 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:36,772 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-10-05 06:26:36,772 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-10-05 06:26:36,773 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,778 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,778 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (99.962 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,779 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,780 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,781 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,782 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,783 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,784 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,785 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,786 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,787 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,788 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,789 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,790 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,791 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,792 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,793 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,794 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,795 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,796 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,797 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,798 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,798 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,798 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,798 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,798 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,798 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,799 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,800 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,801 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,802 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,803 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,804 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,804 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,804 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,804 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,805 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,805 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,805 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,805 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,805 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,805 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,806 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,807 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,808 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,809 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,810 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,811 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,812 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,813 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,814 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,815 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,816 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,817 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,818 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,819 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,820 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,821 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,822 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,823 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,824 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,825 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,826 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,827 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,828 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,829 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,830 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,831 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,832 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,833 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,834 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,835 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,836 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,837 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,838 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,839 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,840 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,841 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,842 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,843 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,844 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,845 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,846 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,847 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,848 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,849 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,850 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,851 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,851 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,852 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,853 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,854 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... 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version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,858 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0, version: 3.3.2.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,859 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,860 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,865 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,865 [pN:job_handler_0,p:8,tN:Thread-1] 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,881 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,882 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,883 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,884 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,885 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (106.426 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0, version: 2.28+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,891 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1, version: 4.9+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.4+galaxy0, version: 2.9.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,892 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0, version: 0.5.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0, version: 3.58.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5, version: 3.36.0+galaxy5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,893 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,894 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,895 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,896 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,897 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,898 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,899 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,900 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,901 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0, version: 2.11.40.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,902 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,903 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,904 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,905 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,906 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,907 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,908 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,909 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,910 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,911 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,912 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,913 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,914 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,915 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,916 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,917 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,918 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,919 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,920 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,921 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,922 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,923 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,924 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,925 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,926 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,927 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,928 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,929 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,930 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,931 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,932 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,933 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,934 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,935 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,936 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,937 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,938 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,939 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,940 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,941 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,942 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,943 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,944 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,945 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,946 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,947 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,948 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,949 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,950 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,951 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,952 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,953 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,954 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,955 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,956 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,957 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,958 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-10-05 06:26:36,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:36,973 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-10-05 06:26:37,007 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (122.243 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,016 [pN:job_handler_0,p:8,tN:Thread-1] 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,021 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, version: 0.0.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,022 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,023 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,024 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0, version: 2.7.11a+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1, version: 2.7.11a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0, version: 1.4.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1, version: 1.8+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.1.1+galaxy1, version: 3.1.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,027 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,028 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy12, version: 0.69.8+galaxy12 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,029 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0, version: 0.2.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,030 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,031 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2, version: 0.5.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,032 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,033 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,034 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1, version: 3.3.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2, version: 3.3.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1, version: 2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1, version: 3.2.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.18.0+galaxy0, version: 3.18.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3, version: 1.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6, version: 0.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/nl/9.3+galaxy1, version: 9.3+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2, version: 9.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/9.3+galaxy1, version: 9.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0, version: 1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,041 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,042 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,043 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0, version: 0.6.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,044 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0, version: 1.24.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, version: 0.23.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,045 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,046 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3, version: 1.20+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.5.2+galaxy0, version: 2.5.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.3+galaxy0, version: 2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2, version: 1.15.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.20+galaxy2, version: 1.20+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5, version: 2.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7, version: 2.1.7 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2, version: 2.5.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2, version: 2.1.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3, version: 2.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.31.1.3, version: 2.31.1.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.31.1, version: 2.31.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0, version: 2.31.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, version: 1.15.1+galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.15.1+galaxy4, version: 1.15.1+galaxy4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1, version: 1.7.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1, version: 1.4.4+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0, version: 1.7.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0, version: 1.43.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, version: 0.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0, version: 1.4.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.3+galaxy1, version: 1.4.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3_r179+galaxy1, version: 0.3_r179+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1, version: 1.5.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1, version: 2.5.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18, version: 0.7.18 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0, version: 0.2.7+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.04.22+galaxy0, version: 1.04.22+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6, version: 4.3+T.galaxy6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2, version: 1.10.1+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1, version: 0.48.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, version: 2.2.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2, version: 2.0.3+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0, version: 1.0.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0rc1+galaxy3, version: 4.0.0rc1+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1, version: 3.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0, version: 3.1.1.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0, version: 1.7.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,089 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,090 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 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DEBUG 2024-10-05 06:26:37,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,099 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0, version: 3.5.4+galaxy0 into tool 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft_add/qiime2__alignment__mafft_add/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mask/qiime2__alignment__mask/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,102 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,132 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-10-05 06:26:37,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-10-05 06:26:37,133 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (124.944 ms) +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-10-05 06:26:37,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:37,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:37,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:37,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-10-05 06:26:37,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-10-05 06:26:37,154 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-10-05 06:26:37,155 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (512.167 ms) +galaxy.queue_worker INFO 2024-10-05 06:26:37,156 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-10-05 06:26:37,157 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.tool_util.deps.containers INFO 2024-10-05 06:26:40,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/datamash:1.8,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:26:40,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/2/tool_script.sh] for tool command [datamash transpose < /galaxy/server/database/objects/7/d/b/dataset_7dbb9727-7b58-466d-9655-008e23538f17.dat > /galaxy/server/database/objects/8/6/6/dataset_86629209-760a-4d6e-92f8-c5c09a837b73.dat] +galaxy.jobs.runners DEBUG 2024-10-05 06:26:40,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (2) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/2/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/2/galaxy_2.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:40,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 2 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:26:40,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:26:40,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1: datamash:1.8 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:26:40,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/datamash:1.8,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:40,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 2 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:40,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:46,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ssh7x with k8s id: gxy-ssh7x succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:26:46,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 2: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:26:55,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 2 finished +galaxy.model.metadata DEBUG 2024-10-05 06:26:55,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.jobs INFO 2024-10-05 06:26:56,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 2 in /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs DEBUG 2024-10-05 06:26:56,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 2 executed (90.696 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:56,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 2 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:26:58,421 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 3 +tpv.core.entities DEBUG 2024-10-05 06:26:58,450 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:26:58,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:26:58,454 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:26:58,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:26:58,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Working directory for job is: /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs.runners DEBUG 2024-10-05 06:26:58,487 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [3] queued (32.758 ms) +galaxy.jobs.handler INFO 2024-10-05 06:26:58,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:58,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 3 +galaxy.jobs DEBUG 2024-10-05 06:26:58,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [3] prepared (73.715 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:26:58,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/3/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/3/registry.xml' '/galaxy/server/database/jobs_directory/000/3/upload_params.json' '3:/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4_files:/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:26:58,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (3) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/3/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/3/galaxy_3.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:58,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 3 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:58,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 3 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:26:58,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:27:20,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8dc68 with k8s id: gxy-8dc68 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:27:20,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 3: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:27:29,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 3 finished +galaxy.model.metadata DEBUG 2024-10-05 06:27:29,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.jobs INFO 2024-10-05 06:27:29,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 3 in /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs DEBUG 2024-10-05 06:27:29,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 3 executed (101.522 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:27:29,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 3 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:27:30,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 4 +tpv.core.entities DEBUG 2024-10-05 06:27:30,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/.*, abstract=False, cores=1, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:27:30,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:27:30,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:27:30,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:27:30,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Working directory for job is: /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs.runners DEBUG 2024-10-05 06:27:30,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [4] queued (44.595 ms) +galaxy.jobs.handler INFO 2024-10-05 06:27:30,134 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:27:30,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 4 +galaxy.security.object_wrapper WARNING 2024-10-05 06:27:30,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to create dynamic subclass SafeStringWrapper__galaxy.model.none_like.None__NoneType__NotImplementedType__Number__SafeStringWrapper__ToolParameterValueWrapper__bool__bytearray__ellipsis for , None: type() doesn't support MRO entry resolution; use types.new_class() +cheetah_DynamicallyCompiledCheetahTemplate_1728109650_200482_91074.py:93: SyntaxWarning: invalid escape sequence '\.' +cheetah_DynamicallyCompiledCheetahTemplate_1728109650_200482_91074.py:124: SyntaxWarning: invalid escape sequence '\.' +galaxy.jobs DEBUG 2024-10-05 06:27:30,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [4] prepared (77.926 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:27:30,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:27:30,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:27:30,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:27:30,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/4/tool_script.sh] for tool command [plotFingerprint --version > /galaxy/server/database/jobs_directory/000/4/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/1/0/4/metadata_104947e0-34a1-43e1-8db9-1cc069aafbe0.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/1/0/4/metadata_104947e0-34a1-43e1-8db9-1cc069aafbe0.dat' './1.bam.bai' && plotFingerprint --numberOfProcessors "${GALAXY_SLOTS:-4}" --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFile /galaxy/server/database/objects/5/d/3/dataset_5d34d069-292e-4b2d-a397-db6ed9e61c4c.dat --plotFileFormat 'png'] +galaxy.jobs.runners DEBUG 2024-10-05 06:27:30,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (4) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/4/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/4/galaxy_4.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:27:30,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:27:30,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:27:30,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:27:30,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:27:30,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:27:31,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:00,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dsdtv failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:00,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:00,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-dsdtv. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:00,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:28:01,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-dsdtv + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-dsdtv": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (4/gxy-dsdtv) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (4/gxy-dsdtv) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (4/gxy-dsdtv) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (4/gxy-dsdtv) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-dsdtv. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Attempting to stop job 4 (gxy-dsdtv) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,033 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Found job with id gxy-dsdtv to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:01,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (4/gxy-dsdtv) Terminated at user's request +galaxy.util WARNING 2024-10-05 06:28:01,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/d/3/dataset_5d34d069-292e-4b2d-a397-db6ed9e61c4c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/d/3/dataset_5d34d069-292e-4b2d-a397-db6ed9e61c4c.dat' +galaxy.jobs.handler DEBUG 2024-10-05 06:28:02,721 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 6, 5 +tpv.core.entities DEBUG 2024-10-05 06:28:02,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:28:02,748 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:28:02,751 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:28:02,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:28:02,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Working directory for job is: /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs.runners DEBUG 2024-10-05 06:28:02,782 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [5] queued (30.628 ms) +galaxy.jobs.handler INFO 2024-10-05 06:28:02,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:02,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 5 +tpv.core.entities DEBUG 2024-10-05 06:28:02,795 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:28:02,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:28:02,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:28:02,815 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:28:02,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Working directory for job is: /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs.runners DEBUG 2024-10-05 06:28:02,848 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [6] queued (48.147 ms) +galaxy.jobs.handler INFO 2024-10-05 06:28:02,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:02,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 6 +galaxy.jobs DEBUG 2024-10-05 06:28:02,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [5] prepared (80.470 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:28:02,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/5/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/5/registry.xml' '/galaxy/server/database/jobs_directory/000/5/upload_params.json' '5:/galaxy/server/database/objects/2/3/b/dataset_23b5e261-9f1c-4307-8650-6e618ef1916e_files:/galaxy/server/database/objects/2/3/b/dataset_23b5e261-9f1c-4307-8650-6e618ef1916e.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:28:02,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (5) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/5/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/5/galaxy_5.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:28:02,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [6] prepared (72.401 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:02,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 5 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:28:02,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/6/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/6/registry.xml' '/galaxy/server/database/jobs_directory/000/6/upload_params.json' '6:/galaxy/server/database/objects/1/e/0/dataset_1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f_files:/galaxy/server/database/objects/1/e/0/dataset_1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:28:02,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (6) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/6/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/6/galaxy_6.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:02,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 5 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:02,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 6 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:02,993 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 6 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:04,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:04,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:14,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qdt55 failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:14,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:14,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-qdt55. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:14,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 6 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (6/gxy-qdt55) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (6/gxy-qdt55) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (6/gxy-qdt55) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (6/gxy-qdt55) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-qdt55. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Attempting to stop job 6 (gxy-qdt55) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Could not find job with id gxy-qdt55 to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:15,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (6/gxy-qdt55) Terminated at user's request +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:16,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dx6kf with k8s id: gxy-dx6kf succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:28:16,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 5: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:28:25,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 5 finished +galaxy.model.metadata DEBUG 2024-10-05 06:28:25,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5 +galaxy.jobs INFO 2024-10-05 06:28:25,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 5 in /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs DEBUG 2024-10-05 06:28:25,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 5 executed (105.668 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:25,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 5 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:28:27,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 7 +tpv.core.entities DEBUG 2024-10-05 06:28:27,320 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:28:27,320 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:28:27,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:28:27,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:28:27,350 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Working directory for job is: /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs.runners DEBUG 2024-10-05 06:28:27,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [7] queued (32.671 ms) +galaxy.jobs.handler INFO 2024-10-05 06:28:27,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:27,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 7 +galaxy.jobs DEBUG 2024-10-05 06:28:27,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [7] prepared (75.696 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:28:27,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/7/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/7/registry.xml' '/galaxy/server/database/jobs_directory/000/7/upload_params.json' '7:/galaxy/server/database/objects/3/8/7/dataset_3877c599-c39a-4b69-8696-b9ac9c8e80fd_files:/galaxy/server/database/objects/3/8/7/dataset_3877c599-c39a-4b69-8696-b9ac9c8e80fd.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:28:27,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (7) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/7/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/7/galaxy_7.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:27,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 7 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:27,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 7 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:28,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:39,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-d5lz6 with k8s id: gxy-d5lz6 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:28:39,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:28:48,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 7 finished +galaxy.model.metadata DEBUG 2024-10-05 06:28:48,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.jobs INFO 2024-10-05 06:28:48,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs DEBUG 2024-10-05 06:28:48,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 7 executed (95.896 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:48,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 7 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:28:49,755 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8 +tpv.core.entities DEBUG 2024-10-05 06:28:49,789 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:28:49,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:28:49,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:28:49,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:28:49,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Working directory for job is: /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs.runners DEBUG 2024-10-05 06:28:49,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [8] queued (36.272 ms) +galaxy.jobs.handler INFO 2024-10-05 06:28:49,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:49,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 8 +galaxy.jobs DEBUG 2024-10-05 06:28:49,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [8] prepared (70.072 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:28:49,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:28:49,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:28:50,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:28:50,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/3/8/7/dataset_3877c599-c39a-4b69-8696-b9ac9c8e80fd.dat' input_single.txt && umi_tools extract --extract-method='string' --bc-pattern='XXXNNN' --3prime --stdin=input_single.txt --stdout '/galaxy/server/database/objects/4/d/1/dataset_4d1de26b-6827-469b-8cb4-d26ee1376ca5.dat' False --quality-filter-threshold '10' --quality-encoding phred33 --log='/galaxy/server/database/objects/3/0/5/dataset_305d1c6a-95b3-4d35-86be-afce4dbac5fe.dat' --log2stderr] +galaxy.jobs.runners DEBUG 2024-10-05 06:28:50,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/8/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/8/galaxy_8.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:50,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 8 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:28:50,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:28:50,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:28:50,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:50,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 8 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:28:50,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:09,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-w2kvf with k8s id: gxy-w2kvf succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:29:10,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 8: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:29:19,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2024-10-05 06:29:19,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.model.metadata DEBUG 2024-10-05 06:29:19,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.jobs INFO 2024-10-05 06:29:19,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 8 in /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs DEBUG 2024-10-05 06:29:19,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 8 executed (81.683 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:19,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 8 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:29:20,379 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 9 +tpv.core.entities DEBUG 2024-10-05 06:29:20,408 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:29:20,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:29:20,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:29:20,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:29:20,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Working directory for job is: /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs.runners DEBUG 2024-10-05 06:29:20,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [9] queued (35.248 ms) +galaxy.jobs.handler INFO 2024-10-05 06:29:20,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:20,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 9 +galaxy.jobs DEBUG 2024-10-05 06:29:20,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [9] prepared (94.052 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:29:20,594 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/9/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/9/registry.xml' '/galaxy/server/database/jobs_directory/000/9/upload_params.json' '10:/galaxy/server/database/objects/8/0/9/dataset_8090a5c8-2cb5-44e7-ade8-d09d43258fc7_files:/galaxy/server/database/objects/8/0/9/dataset_8090a5c8-2cb5-44e7-ade8-d09d43258fc7.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:29:20,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (9) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/9/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/9/galaxy_9.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:20,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 9 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:20,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 9 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:20,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:29:21,454 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 10 +tpv.core.entities DEBUG 2024-10-05 06:29:21,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:29:21,481 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:29:21,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:29:21,495 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:29:21,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Working directory for job is: /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs.runners DEBUG 2024-10-05 06:29:21,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [10] queued (32.058 ms) +galaxy.jobs.handler INFO 2024-10-05 06:29:21,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:21,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 10 +galaxy.jobs DEBUG 2024-10-05 06:29:21,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [10] prepared (75.109 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:29:21,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/10/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/10/registry.xml' '/galaxy/server/database/jobs_directory/000/10/upload_params.json' '11:/galaxy/server/database/objects/a/9/6/dataset_a96c3361-00f2-4649-98ad-936382f452e8_files:/galaxy/server/database/objects/a/9/6/dataset_a96c3361-00f2-4649-98ad-936382f452e8.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:29:21,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (10) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/10/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/10/galaxy_10.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:21,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 10 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:21,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 10 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:21,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:31,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5hppb with k8s id: gxy-5hppb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:29:31,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 9: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:32,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-799lt with k8s id: gxy-799lt succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:29:32,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 10: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:29:40,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 9 finished +galaxy.model.metadata DEBUG 2024-10-05 06:29:40,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.jobs INFO 2024-10-05 06:29:40,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 9 in /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs DEBUG 2024-10-05 06:29:40,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 9 executed (149.873 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:40,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 9 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:29:41,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 10 finished +galaxy.model.metadata DEBUG 2024-10-05 06:29:41,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2024-10-05 06:29:41,868 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 10 in /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs DEBUG 2024-10-05 06:29:41,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 10 executed (81.607 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:41,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 10 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:29:42,926 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11 +tpv.core.entities DEBUG 2024-10-05 06:29:42,959 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:29:42,960 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:29:42,964 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:29:42,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:29:43,000 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Working directory for job is: /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs.runners DEBUG 2024-10-05 06:29:43,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [11] queued (45.032 ms) +galaxy.jobs.handler INFO 2024-10-05 06:29:43,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:43,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 11 +galaxy.jobs DEBUG 2024-10-05 06:29:43,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [11] prepared (55.448 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:29:43,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:29:43,078 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:29:43,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:29:43,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/11/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/8/0/9/dataset_8090a5c8-2cb5-44e7-ade8-d09d43258fc7.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/a/9/6/dataset_a96c3361-00f2-4649-98ad-936382f452e8.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log='/galaxy/server/database/objects/f/9/a/dataset_f9a7ad67-99cb-47c4-a3c0-f3f392bdfa20.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/c/1/b/dataset_c1b868eb-00b9-4115-9b08-655e99c8a643.dat' && mv out2.gz '/galaxy/server/database/objects/4/9/1/dataset_491a36e4-1b8b-4488-bd21-6d6c7a4db432.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:29:43,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (11) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/11/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/11/galaxy_11.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:43,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 11 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:29:43,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:29:43,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:29:43,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:43,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 11 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:44,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:49,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kb6sx with k8s id: gxy-kb6sx succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:29:49,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 11: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:29:58,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 11 finished +galaxy.model.metadata DEBUG 2024-10-05 06:29:58,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.model.metadata DEBUG 2024-10-05 06:29:58,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.model.metadata DEBUG 2024-10-05 06:29:58,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.util WARNING 2024-10-05 06:29:58,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/9/1/dataset_491a36e4-1b8b-4488-bd21-6d6c7a4db432.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/9/1/dataset_491a36e4-1b8b-4488-bd21-6d6c7a4db432.dat' +galaxy.util WARNING 2024-10-05 06:29:58,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/1/b/dataset_c1b868eb-00b9-4115-9b08-655e99c8a643.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/1/b/dataset_c1b868eb-00b9-4115-9b08-655e99c8a643.dat' +galaxy.jobs INFO 2024-10-05 06:29:58,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 11 in /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs DEBUG 2024-10-05 06:29:58,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 11 executed (92.927 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:29:58,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 11 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:30:01,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 12, 13 +tpv.core.entities DEBUG 2024-10-05 06:30:01,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:30:01,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:30:01,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:30:01,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:30:01,402 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Working directory for job is: /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs.runners DEBUG 2024-10-05 06:30:01,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [12] queued (33.947 ms) +galaxy.jobs.handler INFO 2024-10-05 06:30:01,411 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:01,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 12 +tpv.core.entities DEBUG 2024-10-05 06:30:01,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:30:01,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:30:01,427 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:30:01,439 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:30:01,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Working directory for job is: /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs.runners DEBUG 2024-10-05 06:30:01,472 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [13] queued (45.088 ms) +galaxy.jobs.handler INFO 2024-10-05 06:30:01,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:01,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 13 +galaxy.jobs DEBUG 2024-10-05 06:30:01,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [12] prepared (87.927 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:30:01,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/12/registry.xml' '/galaxy/server/database/jobs_directory/000/12/upload_params.json' '15:/galaxy/server/database/objects/6/e/6/dataset_6e627e9d-74b3-4422-8856-e9d2502212ca_files:/galaxy/server/database/objects/6/e/6/dataset_6e627e9d-74b3-4422-8856-e9d2502212ca.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:30:01,552 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (12) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/12/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/12/galaxy_12.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:01,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 12 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:30:01,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [13] prepared (81.901 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:01,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 12 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:30:01,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/13/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '16:/galaxy/server/database/objects/9/f/6/dataset_9f691063-3e38-4133-82d2-d29c45e6e414_files:/galaxy/server/database/objects/9/f/6/dataset_9f691063-3e38-4133-82d2-d29c45e6e414.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:30:01,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (13) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/13/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/13/galaxy_13.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:01,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 13 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:01,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 13 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:02,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:02,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:12,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qhflw with k8s id: gxy-qhflw succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:12,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wvkwx with k8s id: gxy-wvkwx succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:30:12,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 12: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:30:12,847 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 13: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:30:22,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 12 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:30:22,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 13 finished +galaxy.model.metadata DEBUG 2024-10-05 06:30:22,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.model.metadata DEBUG 2024-10-05 06:30:22,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 16 +galaxy.jobs INFO 2024-10-05 06:30:22,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 12 in /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs INFO 2024-10-05 06:30:22,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 13 in /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs DEBUG 2024-10-05 06:30:22,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 12 executed (132.464 ms) +galaxy.jobs DEBUG 2024-10-05 06:30:22,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 13 executed (113.699 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:22,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 12 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:22,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 13 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:30:23,931 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2024-10-05 06:30:23,963 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:30:23,964 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:30:23,968 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:30:23,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:30:24,001 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Working directory for job is: /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs.runners DEBUG 2024-10-05 06:30:24,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [14] queued (42.455 ms) +galaxy.jobs.handler INFO 2024-10-05 06:30:24,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:24,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 14 +galaxy.tools.evaluation INFO 2024-10-05 06:30:24,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Updating param_dict for forward with /galaxy/server/database/objects/3/3/4/dataset_334eaa00-c2f1-4e99-8562-11ea97e9fd15.dat +galaxy.tools.evaluation INFO 2024-10-05 06:30:24,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Updating param_dict for reverse with /galaxy/server/database/objects/4/4/a/dataset_44ad62d0-76dd-448b-9ea9-89fa8a841516.dat +galaxy.jobs DEBUG 2024-10-05 06:30:24,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [14] prepared (79.685 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:30:24,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:30:24,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:30:24,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:30:24,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/6/e/6/dataset_6e627e9d-74b3-4422-8856-e9d2502212ca.dat' input_read1.txt && ln -s '/galaxy/server/database/objects/9/f/6/dataset_9f691063-3e38-4133-82d2-d29c45e6e414.dat' input_read2.txt && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.txt --read2-in=input_read2.txt --stdout '/galaxy/server/database/objects/3/3/4/dataset_334eaa00-c2f1-4e99-8562-11ea97e9fd15.dat' --read2-out='/galaxy/server/database/objects/4/4/a/dataset_44ad62d0-76dd-448b-9ea9-89fa8a841516.dat' False --log='/galaxy/server/database/objects/a/0/b/dataset_a0bd9382-0e4b-4765-ace6-d97e06ed4593.dat' --log2stderr] +galaxy.jobs.runners DEBUG 2024-10-05 06:30:24,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (14) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/14/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/14/galaxy_14.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:24,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 14 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:30:24,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:30:24,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:30:24,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:24,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 14 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:24,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:30,860 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-x7g9k with k8s id: gxy-x7g9k succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:30:31,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 14: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:30:39,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2024-10-05 06:30:39,984 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.model.metadata DEBUG 2024-10-05 06:30:39,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.model.metadata DEBUG 2024-10-05 06:30:40,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.jobs INFO 2024-10-05 06:30:40,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs DEBUG 2024-10-05 06:30:40,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 14 executed (110.593 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:40,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 14 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:30:42,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 15, 17, 16 +tpv.core.entities DEBUG 2024-10-05 06:30:42,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:30:42,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:30:42,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:30:42,573 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:30:42,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Working directory for job is: /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs.runners DEBUG 2024-10-05 06:30:42,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [15] queued (33.479 ms) +galaxy.jobs.handler INFO 2024-10-05 06:30:42,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 15 +tpv.core.entities DEBUG 2024-10-05 06:30:42,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:30:42,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:30:42,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:30:42,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:30:42,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Working directory for job is: /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs.runners DEBUG 2024-10-05 06:30:42,664 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [17] queued (49.571 ms) +galaxy.jobs.handler INFO 2024-10-05 06:30:42,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 17 +tpv.core.entities DEBUG 2024-10-05 06:30:42,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:30:42,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:30:42,693 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:30:42,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:30:42,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [15] prepared (110.044 ms) +galaxy.jobs DEBUG 2024-10-05 06:30:42,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Working directory for job is: /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs.runners DEBUG 2024-10-05 06:30:42,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [16] queued (61.514 ms) +galaxy.jobs.handler INFO 2024-10-05 06:30:42,757 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 16 +galaxy.jobs.command_factory INFO 2024-10-05 06:30:42,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/15/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/15/registry.xml' '/galaxy/server/database/jobs_directory/000/15/upload_params.json' '20:/galaxy/server/database/objects/3/b/9/dataset_3b9bf2ee-67c5-4640-a976-3de8a54f0358_files:/galaxy/server/database/objects/3/b/9/dataset_3b9bf2ee-67c5-4640-a976-3de8a54f0358.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:30:42,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (15) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/15/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/15/galaxy_15.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 15 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:30:42,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [17] prepared (118.446 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 15 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:30:42,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/17/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/17/registry.xml' '/galaxy/server/database/jobs_directory/000/17/upload_params.json' '22:/galaxy/server/database/objects/d/1/2/dataset_d12f8555-e011-4ca5-92f3-71d30d1f482d_files:/galaxy/server/database/objects/d/1/2/dataset_d12f8555-e011-4ca5-92f3-71d30d1f482d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:30:42,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (17) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/17/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/17/galaxy_17.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:30:42,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [16] prepared (88.241 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 17 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 17 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:30:42,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/16/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/16/registry.xml' '/galaxy/server/database/jobs_directory/000/16/upload_params.json' '21:/galaxy/server/database/objects/2/4/3/dataset_243a9aae-de47-4eef-978c-68d2696fe71b_files:/galaxy/server/database/objects/2/4/3/dataset_243a9aae-de47-4eef-978c-68d2696fe71b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:30:42,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (16) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/16/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/16/galaxy_16.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:42,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:43,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:44,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:44,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:54,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-f6wnr with k8s id: gxy-f6wnr succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:54,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-swtfn with k8s id: gxy-swtfn succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:30:54,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qt4dg with k8s id: gxy-qt4dg succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:30:54,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 15: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:30:54,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 16: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:30:54,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:31:08,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 15 finished +galaxy.model.metadata DEBUG 2024-10-05 06:31:08,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.jobs INFO 2024-10-05 06:31:08,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 15 in /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs DEBUG 2024-10-05 06:31:08,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 15 executed (136.634 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:08,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 15 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:08,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 16 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:31:08,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2024-10-05 06:31:08,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.model.metadata DEBUG 2024-10-05 06:31:08,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.jobs INFO 2024-10-05 06:31:08,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 16 in /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs INFO 2024-10-05 06:31:09,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2024-10-05 06:31:09,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 16 executed (113.831 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:09,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:31:09,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 17 executed (116.726 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:09,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 17 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:31:09,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 18 +tpv.core.entities DEBUG 2024-10-05 06:31:09,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:31:09,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:31:09,436 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:31:09,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:31:09,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Working directory for job is: /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs.runners DEBUG 2024-10-05 06:31:09,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [18] queued (40.909 ms) +galaxy.jobs.handler INFO 2024-10-05 06:31:09,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:09,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 18 +galaxy.jobs DEBUG 2024-10-05 06:31:09,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [18] prepared (57.431 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:31:09,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:31:09,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:31:09,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:31:09,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/3/b/9/dataset_3b9bf2ee-67c5-4640-a976-3de8a54f0358.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/2/4/3/dataset_243a9aae-de47-4eef-978c-68d2696fe71b.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='CCCCCCNNNNNNNNNN' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/d/1/2/dataset_d12f8555-e011-4ca5-92f3-71d30d1f482d.dat' False --log='/galaxy/server/database/objects/d/f/d/dataset_dfd0e038-6ced-4819-9c8b-1ebe24397723.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/1/1/a/dataset_11a729f9-9bda-45dd-9deb-ee5c2c8df986.dat' && mv out2.gz '/galaxy/server/database/objects/a/0/9/dataset_a091f503-86aa-440c-974d-8d6b1b854e73.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:09,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (18) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/18/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/18/galaxy_18.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:09,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:31:09,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:31:09,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:31:09,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:09,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:10,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:15,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-k8d8t with k8s id: gxy-k8d8t succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:31:15,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 18: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:31:25,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 18 finished +galaxy.model.metadata DEBUG 2024-10-05 06:31:25,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.model.metadata DEBUG 2024-10-05 06:31:25,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.model.metadata DEBUG 2024-10-05 06:31:25,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 25 +galaxy.util WARNING 2024-10-05 06:31:25,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/1/a/dataset_11a729f9-9bda-45dd-9deb-ee5c2c8df986.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/1/a/dataset_11a729f9-9bda-45dd-9deb-ee5c2c8df986.dat' +galaxy.util WARNING 2024-10-05 06:31:25,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/0/9/dataset_a091f503-86aa-440c-974d-8d6b1b854e73.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/0/9/dataset_a091f503-86aa-440c-974d-8d6b1b854e73.dat' +galaxy.jobs INFO 2024-10-05 06:31:25,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 18 in /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs DEBUG 2024-10-05 06:31:25,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 18 executed (96.286 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:25,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:31:26,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 19 +tpv.core.entities DEBUG 2024-10-05 06:31:26,833 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:31:26,834 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:31:26,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:31:26,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:31:26,862 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Working directory for job is: /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs.runners DEBUG 2024-10-05 06:31:26,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [19] queued (31.511 ms) +galaxy.jobs.handler INFO 2024-10-05 06:31:26,872 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:26,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 19 +galaxy.jobs DEBUG 2024-10-05 06:31:26,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [19] prepared (75.380 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:31:26,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/19/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/19/registry.xml' '/galaxy/server/database/jobs_directory/000/19/upload_params.json' '26:/galaxy/server/database/objects/8/9/1/dataset_891c62e7-39a8-47bd-9982-130c20cb4662_files:/galaxy/server/database/objects/8/9/1/dataset_891c62e7-39a8-47bd-9982-130c20cb4662.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:26,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (19) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/19/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/19/galaxy_19.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:26,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:27,014 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:27,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:31:27,876 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 20, 21 +tpv.core.entities DEBUG 2024-10-05 06:31:27,901 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:31:27,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:31:27,905 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:31:27,917 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:31:27,931 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Working directory for job is: /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs.runners DEBUG 2024-10-05 06:31:27,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [20] queued (32.689 ms) +galaxy.jobs.handler INFO 2024-10-05 06:31:27,940 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:27,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 20 +tpv.core.entities DEBUG 2024-10-05 06:31:27,953 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:31:27,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:31:27,958 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:31:27,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:31:27,994 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Working directory for job is: /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs.runners DEBUG 2024-10-05 06:31:28,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [21] queued (43.945 ms) +galaxy.jobs.handler INFO 2024-10-05 06:31:28,005 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 21 +galaxy.jobs DEBUG 2024-10-05 06:31:28,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [20] prepared (104.451 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:31:28,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/20/registry.xml' '/galaxy/server/database/jobs_directory/000/20/upload_params.json' '27:/galaxy/server/database/objects/f/5/c/dataset_f5cae9d0-9027-4be9-a738-219318740c0d_files:/galaxy/server/database/objects/f/5/c/dataset_f5cae9d0-9027-4be9-a738-219318740c0d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:28,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (20) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/20/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/20/galaxy_20.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:31:28,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [21] prepared (84.202 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 20 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 20 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:31:28,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/21/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/21/registry.xml' '/galaxy/server/database/jobs_directory/000/21/upload_params.json' '28:/galaxy/server/database/objects/3/5/9/dataset_359f6757-453d-4e19-b1ae-80ce70c6e840_files:/galaxy/server/database/objects/3/5/9/dataset_359f6757-453d-4e19-b1ae-80ce70c6e840.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:28,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (21) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/21/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/21/galaxy_21.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 21 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 21 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:28,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2r224 failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-2r224. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:31:38,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-2r224 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-2r224": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-m7vd5 with k8s id: gxy-m7vd5 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (19/gxy-2r224) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (19/gxy-2r224) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (19/gxy-2r224) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (19/gxy-2r224) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-2r224. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Attempting to stop job 19 (gxy-2r224) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Found job with id gxy-2r224 to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:38,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (19/gxy-2r224) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-10-05 06:31:38,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 20: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.handler DEBUG 2024-10-05 06:31:39,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 22, 23 +tpv.core.entities DEBUG 2024-10-05 06:31:39,250 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:31:39,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:31:39,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:31:39,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:31:39,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Working directory for job is: /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs.runners DEBUG 2024-10-05 06:31:39,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [22] queued (34.915 ms) +galaxy.jobs.handler INFO 2024-10-05 06:31:39,293 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 22 +tpv.core.entities DEBUG 2024-10-05 06:31:39,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:31:39,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:31:39,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:31:39,323 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:31:39,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Working directory for job is: /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs.runners DEBUG 2024-10-05 06:31:39,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [23] queued (42.809 ms) +galaxy.jobs.handler INFO 2024-10-05 06:31:39,358 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 23 +galaxy.jobs DEBUG 2024-10-05 06:31:39,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [22] prepared (98.855 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-98qxx with k8s id: gxy-98qxx succeeded +galaxy.jobs.command_factory INFO 2024-10-05 06:31:39,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/22/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/22/registry.xml' '/galaxy/server/database/jobs_directory/000/22/upload_params.json' '29:/galaxy/server/database/objects/9/c/5/dataset_9c554cb8-32c9-475e-93db-5496c4f245fb_files:/galaxy/server/database/objects/9/c/5/dataset_9c554cb8-32c9-475e-93db-5496c4f245fb.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:39,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (22) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/22/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/22/galaxy_22.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:31:39,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [23] prepared (90.037 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 22 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:31:39,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/23/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/23/registry.xml' '/galaxy/server/database/jobs_directory/000/23/upload_params.json' '30:/galaxy/server/database/objects/b/8/d/dataset_b8d00482-145c-44ac-8530-1a40c4fa5271_files:/galaxy/server/database/objects/b/8/d/dataset_b8d00482-145c-44ac-8530-1a40c4fa5271.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 22 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:39,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (23) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/23/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/23/galaxy_23.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 23 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:39,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 23 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:39,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:40,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:40,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners DEBUG 2024-10-05 06:31:48,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 20 finished +galaxy.model.metadata DEBUG 2024-10-05 06:31:48,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 27 +galaxy.jobs INFO 2024-10-05 06:31:48,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 20 in /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs DEBUG 2024-10-05 06:31:48,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 20 executed (103.841 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:48,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 20 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:31:49,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2024-10-05 06:31:49,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.jobs INFO 2024-10-05 06:31:49,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 21 in /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs DEBUG 2024-10-05 06:31:49,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 21 executed (91.281 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:49,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 21 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:50,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qpf6v with k8s id: gxy-qpf6v succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:31:50,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dsd2d with k8s id: gxy-dsd2d succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:31:51,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 22: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:31:51,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 23: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:32:00,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 23 finished +galaxy.model.metadata DEBUG 2024-10-05 06:32:00,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.jobs INFO 2024-10-05 06:32:00,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 23 in /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs.runners DEBUG 2024-10-05 06:32:00,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 22 finished +galaxy.model.metadata DEBUG 2024-10-05 06:32:00,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.jobs DEBUG 2024-10-05 06:32:00,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 23 executed (199.033 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:00,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 23 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs INFO 2024-10-05 06:32:00,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 22 in /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs DEBUG 2024-10-05 06:32:00,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 22 executed (174.909 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:00,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 22 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:32:00,940 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 24 +tpv.core.entities DEBUG 2024-10-05 06:32:00,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:32:00,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:32:00,979 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:32:00,990 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:32:01,005 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Working directory for job is: /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs.runners DEBUG 2024-10-05 06:32:01,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [24] queued (36.203 ms) +galaxy.jobs.handler INFO 2024-10-05 06:32:01,017 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:01,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 24 +galaxy.jobs DEBUG 2024-10-05 06:32:01,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [24] prepared (56.112 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:01,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:32:01,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:01,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:32:01,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/24/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/c/5/dataset_9c554cb8-32c9-475e-93db-5496c4f245fb.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/b/8/d/dataset_b8d00482-145c-44ac-8530-1a40c4fa5271.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/4/c/f/dataset_4cff3bb0-bf00-482a-8a0c-0fd33cc7578f.dat' && mv out2.gz '/galaxy/server/database/objects/d/5/9/dataset_d5926650-4696-4738-8471-d9ab25977335.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:32:01,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (24) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/24/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/24/galaxy_24.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:01,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 24 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:01,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:32:01,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:01,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:01,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 24 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:01,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:08,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-m6sqb with k8s id: gxy-m6sqb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:32:08,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 24: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:32:17,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 24 finished +galaxy.model.metadata DEBUG 2024-10-05 06:32:17,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.model.metadata DEBUG 2024-10-05 06:32:17,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.util WARNING 2024-10-05 06:32:17,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/c/f/dataset_4cff3bb0-bf00-482a-8a0c-0fd33cc7578f.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/c/f/dataset_4cff3bb0-bf00-482a-8a0c-0fd33cc7578f.dat' +galaxy.util WARNING 2024-10-05 06:32:17,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/d/5/9/dataset_d5926650-4696-4738-8471-d9ab25977335.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/d/5/9/dataset_d5926650-4696-4738-8471-d9ab25977335.dat' +galaxy.jobs INFO 2024-10-05 06:32:17,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2024-10-05 06:32:17,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 24 executed (82.728 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:17,515 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 24 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:32:20,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 25 +tpv.core.entities DEBUG 2024-10-05 06:32:20,399 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:32:20,399 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:32:20,403 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:32:20,417 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:32:20,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Working directory for job is: /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs.runners DEBUG 2024-10-05 06:32:20,440 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [25] queued (36.568 ms) +galaxy.jobs.handler INFO 2024-10-05 06:32:20,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:20,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 25 +galaxy.jobs DEBUG 2024-10-05 06:32:20,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [25] prepared (92.948 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:32:20,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/25/registry.xml' '/galaxy/server/database/jobs_directory/000/25/upload_params.json' '33:/galaxy/server/database/objects/1/7/8/dataset_178ab2a4-b67e-47b8-b5af-e827855ce288_files:/galaxy/server/database/objects/1/7/8/dataset_178ab2a4-b67e-47b8-b5af-e827855ce288.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:32:20,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (25) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/25/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/25/galaxy_25.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:20,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 25 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:20,630 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 25 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:21,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:32,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-98rhw with k8s id: gxy-98rhw succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:32:32,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 25: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:32:41,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 25 finished +galaxy.model.metadata DEBUG 2024-10-05 06:32:42,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.jobs INFO 2024-10-05 06:32:42,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 25 in /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs DEBUG 2024-10-05 06:32:42,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 25 executed (94.487 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:42,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 25 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:32:43,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 26 +tpv.core.entities DEBUG 2024-10-05 06:32:43,044 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:32:43,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:32:43,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:32:43,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:32:43,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Working directory for job is: /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs.runners DEBUG 2024-10-05 06:32:43,086 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [26] queued (37.934 ms) +galaxy.jobs.handler INFO 2024-10-05 06:32:43,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:43,091 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 26 +galaxy.jobs DEBUG 2024-10-05 06:32:43,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [26] prepared (52.002 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:43,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:32:43,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:43,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:32:43,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/26/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/1/7/8/dataset_178ab2a4-b67e-47b8-b5af-e827855ce288.dat' input_single.txt && umi_tools extract --extract-method='string' --bc-pattern='XXXNNN' --3prime --stdin=input_single.txt --stdout '/galaxy/server/database/objects/b/8/8/dataset_b88e14ea-c018-4d42-8f3d-63db288a6fb8.dat' False --quality-filter-threshold '10' --quality-encoding phred33 --log='/galaxy/server/database/objects/0/f/d/dataset_0fd26597-e498-4a4e-bd95-b035107a2a41.dat' --log2stderr] +galaxy.jobs.runners DEBUG 2024-10-05 06:32:43,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (26) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/26/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/26/galaxy_26.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:43,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 26 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:43,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:32:43,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:32:43,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:43,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 26 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:44,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:49,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zkdbp with k8s id: gxy-zkdbp succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:32:49,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 26: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:32:58,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 26 finished +galaxy.model.metadata DEBUG 2024-10-05 06:32:58,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.model.metadata DEBUG 2024-10-05 06:32:58,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.jobs INFO 2024-10-05 06:32:58,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 26 in /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs DEBUG 2024-10-05 06:32:58,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 26 executed (80.964 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:32:58,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 26 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:33:00,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 27 +tpv.core.entities DEBUG 2024-10-05 06:33:00,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:33:00,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:33:00,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:33:00,472 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:33:00,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Working directory for job is: /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs.runners DEBUG 2024-10-05 06:33:00,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [27] queued (49.263 ms) +galaxy.jobs.handler INFO 2024-10-05 06:33:00,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:00,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 27 +galaxy.jobs DEBUG 2024-10-05 06:33:00,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [27] prepared (94.562 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:33:00,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/27/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/27/registry.xml' '/galaxy/server/database/jobs_directory/000/27/upload_params.json' '36:/galaxy/server/database/objects/0/a/0/dataset_0a08dbcd-c26e-4967-9a4e-4e671e289539_files:/galaxy/server/database/objects/0/a/0/dataset_0a08dbcd-c26e-4967-9a4e-4e671e289539.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:33:00,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (27) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/27/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/27/galaxy_27.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:00,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:00,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:33:01,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 28 +tpv.core.entities DEBUG 2024-10-05 06:33:01,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:33:01,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:33:01,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:01,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs DEBUG 2024-10-05 06:33:01,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:33:01,568 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Working directory for job is: /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs.runners DEBUG 2024-10-05 06:33:01,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [28] queued (41.470 ms) +galaxy.jobs.handler INFO 2024-10-05 06:33:01,578 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:01,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 28 +galaxy.jobs DEBUG 2024-10-05 06:33:01,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [28] prepared (74.223 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:33:01,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/28/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/28/registry.xml' '/galaxy/server/database/jobs_directory/000/28/upload_params.json' '37:/galaxy/server/database/objects/c/8/1/dataset_c8106b22-d925-40a5-874b-8fcba90745f1_files:/galaxy/server/database/objects/c/8/1/dataset_c8106b22-d925-40a5-874b-8fcba90745f1.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:33:01,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (28) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/28/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/28/galaxy_28.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:01,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 28 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:01,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 28 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:02,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:11,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vqrwx with k8s id: gxy-vqrwx succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:33:11,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 27: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:12,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-prwjp with k8s id: gxy-prwjp succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:33:13,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 28: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:33:21,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 27 finished +galaxy.model.metadata DEBUG 2024-10-05 06:33:21,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.jobs INFO 2024-10-05 06:33:21,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 27 in /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs DEBUG 2024-10-05 06:33:21,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 27 executed (90.080 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:21,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:33:22,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 28 finished +galaxy.model.metadata DEBUG 2024-10-05 06:33:22,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.jobs INFO 2024-10-05 06:33:22,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 28 in /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs DEBUG 2024-10-05 06:33:22,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 28 executed (80.757 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:22,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 28 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:33:23,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2024-10-05 06:33:23,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:33:23,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:33:23,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:33:23,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:33:23,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Working directory for job is: /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs.runners DEBUG 2024-10-05 06:33:23,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [29] queued (40.489 ms) +galaxy.jobs.handler INFO 2024-10-05 06:33:23,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:23,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 29 +galaxy.jobs DEBUG 2024-10-05 06:33:23,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [29] prepared (54.107 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:33:23,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:33:23,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:33:23,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:33:23,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/29/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/0/a/0/dataset_0a08dbcd-c26e-4967-9a4e-4e671e289539.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/c/8/1/dataset_c8106b22-d925-40a5-874b-8fcba90745f1.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log='/galaxy/server/database/objects/e/6/4/dataset_e64d4a4a-f1ee-4c47-bcea-45a1eb4d67ac.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/7/f/9/dataset_7f9707e1-71cf-45d7-96df-2af1e3d2870d.dat' && mv out2.gz '/galaxy/server/database/objects/6/8/3/dataset_68362aa5-c129-4588-ada7-0bc69bd9b1b5.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:33:23,240 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (29) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/29/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/29/galaxy_29.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:23,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 29 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:33:23,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:33:23,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:33:23,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:23,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 29 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:23,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:29,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-55x65 with k8s id: gxy-55x65 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:33:29,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 29: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:33:38,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 29 finished +galaxy.model.metadata DEBUG 2024-10-05 06:33:38,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.model.metadata DEBUG 2024-10-05 06:33:38,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.model.metadata DEBUG 2024-10-05 06:33:38,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.util WARNING 2024-10-05 06:33:38,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/7/f/9/dataset_7f9707e1-71cf-45d7-96df-2af1e3d2870d.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/7/f/9/dataset_7f9707e1-71cf-45d7-96df-2af1e3d2870d.dat' +galaxy.util WARNING 2024-10-05 06:33:38,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/8/3/dataset_68362aa5-c129-4588-ada7-0bc69bd9b1b5.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/8/3/dataset_68362aa5-c129-4588-ada7-0bc69bd9b1b5.dat' +galaxy.jobs INFO 2024-10-05 06:33:38,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 29 in /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs DEBUG 2024-10-05 06:33:38,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 29 executed (97.853 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:38,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 29 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:33:40,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30, 31 +tpv.core.entities DEBUG 2024-10-05 06:33:40,488 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:33:40,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:33:40,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:33:40,504 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:33:40,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Working directory for job is: /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs.runners DEBUG 2024-10-05 06:33:40,526 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [30] queued (33.045 ms) +galaxy.jobs.handler INFO 2024-10-05 06:33:40,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:40,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 30 +tpv.core.entities DEBUG 2024-10-05 06:33:40,541 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:33:40,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:33:40,546 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:33:40,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:33:40,610 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Working directory for job is: /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs.runners DEBUG 2024-10-05 06:33:40,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [31] queued (71.947 ms) +galaxy.jobs.handler INFO 2024-10-05 06:33:40,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:40,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 31 +galaxy.jobs DEBUG 2024-10-05 06:33:40,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [30] prepared (118.562 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:33:40,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/30/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/30/registry.xml' '/galaxy/server/database/jobs_directory/000/30/upload_params.json' '41:/galaxy/server/database/objects/e/8/f/dataset_e8f57275-5a01-49cd-9cf5-111b9a830743_files:/galaxy/server/database/objects/e/8/f/dataset_e8f57275-5a01-49cd-9cf5-111b9a830743.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:33:40,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (30) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/30/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/30/galaxy_30.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:33:40,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [31] prepared (76.655 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:40,712 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 30 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:40,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 30 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:33:40,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/31/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/31/registry.xml' '/galaxy/server/database/jobs_directory/000/31/upload_params.json' '42:/galaxy/server/database/objects/c/4/8/dataset_c483f840-7f8d-4fea-82c7-a43c693039e4_files:/galaxy/server/database/objects/c/4/8/dataset_c483f840-7f8d-4fea-82c7-a43c693039e4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:33:40,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (31) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/31/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/31/galaxy_31.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:40,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 31 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:40,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 31 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:41,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:41,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:52,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cx44l with k8s id: gxy-cx44l succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:33:52,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pf9d6 with k8s id: gxy-pf9d6 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:33:52,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 30: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:33:52,526 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 31: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:34:01,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 30 finished +galaxy.model.metadata DEBUG 2024-10-05 06:34:01,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 41 +galaxy.jobs.runners DEBUG 2024-10-05 06:34:02,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 31 finished +galaxy.jobs INFO 2024-10-05 06:34:02,033 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 30 in /galaxy/server/database/jobs_directory/000/30 +galaxy.model.metadata DEBUG 2024-10-05 06:34:02,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 42 +galaxy.jobs INFO 2024-10-05 06:34:02,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 31 in /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs DEBUG 2024-10-05 06:34:02,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 30 executed (122.865 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:02,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 30 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:34:02,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 31 executed (115.085 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:02,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 31 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:34:03,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 32 +tpv.core.entities DEBUG 2024-10-05 06:34:03,153 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:34:03,154 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:34:03,157 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:34:03,170 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:34:03,188 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Working directory for job is: /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs.runners DEBUG 2024-10-05 06:34:03,197 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [32] queued (39.859 ms) +galaxy.jobs.handler INFO 2024-10-05 06:34:03,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:03,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 32 +galaxy.tools.evaluation INFO 2024-10-05 06:34:03,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Updating param_dict for forward with /galaxy/server/database/objects/b/e/4/dataset_be474794-4e6b-4f01-a6fa-9a8d42516fb3.dat +galaxy.tools.evaluation INFO 2024-10-05 06:34:03,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Updating param_dict for reverse with /galaxy/server/database/objects/d/6/2/dataset_d62e4a59-50a1-47b4-8d0d-32dab8b24ad7.dat +galaxy.jobs DEBUG 2024-10-05 06:34:03,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [32] prepared (65.491 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:03,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:34:03,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:03,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:34:03,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/32/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/e/8/f/dataset_e8f57275-5a01-49cd-9cf5-111b9a830743.dat' input_read1.txt && ln -s '/galaxy/server/database/objects/c/4/8/dataset_c483f840-7f8d-4fea-82c7-a43c693039e4.dat' input_read2.txt && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.txt --read2-in=input_read2.txt --stdout '/galaxy/server/database/objects/b/e/4/dataset_be474794-4e6b-4f01-a6fa-9a8d42516fb3.dat' --read2-out='/galaxy/server/database/objects/d/6/2/dataset_d62e4a59-50a1-47b4-8d0d-32dab8b24ad7.dat' False --log='/galaxy/server/database/objects/9/4/2/dataset_942322d6-442b-4371-ad9e-5fe5980d351e.dat' --log2stderr] +galaxy.jobs.runners DEBUG 2024-10-05 06:34:03,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (32) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/32/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/32/galaxy_32.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:03,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 32 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:03,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:34:03,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:03,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:03,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 32 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:04,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:09,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hmzdm with k8s id: gxy-hmzdm succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:34:09,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:34:18,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 32 finished +galaxy.model.metadata DEBUG 2024-10-05 06:34:18,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.model.metadata DEBUG 2024-10-05 06:34:18,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.model.metadata DEBUG 2024-10-05 06:34:18,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.jobs INFO 2024-10-05 06:34:18,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 32 in /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs DEBUG 2024-10-05 06:34:19,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 32 executed (99.730 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:19,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 32 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:34:20,550 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 33 +tpv.core.entities DEBUG 2024-10-05 06:34:20,577 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:34:20,578 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:34:20,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:34:20,593 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:34:20,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Working directory for job is: /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs.runners DEBUG 2024-10-05 06:34:20,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [33] queued (31.937 ms) +galaxy.jobs.handler INFO 2024-10-05 06:34:20,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:20,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 33 +galaxy.jobs DEBUG 2024-10-05 06:34:20,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [33] prepared (71.787 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:34:20,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/33/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/33/registry.xml' '/galaxy/server/database/jobs_directory/000/33/upload_params.json' '46:/galaxy/server/database/objects/3/f/f/dataset_3ffddad1-502f-4a96-970a-31846931e9e1_files:/galaxy/server/database/objects/3/f/f/dataset_3ffddad1-502f-4a96-970a-31846931e9e1.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:34:20,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (33) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/33/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/33/galaxy_33.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:20,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 33 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:20,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 33 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:34:21,620 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 35, 34 +tpv.core.entities DEBUG 2024-10-05 06:34:21,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:34:21,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:34:21,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:34:21,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:34:21,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Working directory for job is: /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs.runners DEBUG 2024-10-05 06:34:21,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [35] queued (32.594 ms) +galaxy.jobs.handler INFO 2024-10-05 06:34:21,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 35 +tpv.core.entities DEBUG 2024-10-05 06:34:21,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:34:21,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:34:21,705 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:34:21,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:34:21,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Working directory for job is: /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs.runners DEBUG 2024-10-05 06:34:21,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [34] queued (44.284 ms) +galaxy.jobs.handler INFO 2024-10-05 06:34:21,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 34 +galaxy.jobs DEBUG 2024-10-05 06:34:21,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [35] prepared (98.019 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:34:21,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/35/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/35/registry.xml' '/galaxy/server/database/jobs_directory/000/35/upload_params.json' '48:/galaxy/server/database/objects/b/d/2/dataset_bd2e62e9-a9f3-4f7e-96c2-91a40ac6e155_files:/galaxy/server/database/objects/b/d/2/dataset_bd2e62e9-a9f3-4f7e-96c2-91a40ac6e155.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:34:21,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (35) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/35/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/35/galaxy_35.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:34:21,847 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [34] prepared (81.067 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 35 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 35 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:34:21,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/34/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/34/registry.xml' '/galaxy/server/database/jobs_directory/000/34/upload_params.json' '47:/galaxy/server/database/objects/6/4/f/dataset_64f0eb5c-7696-44cb-af7f-1fb99383107f_files:/galaxy/server/database/objects/6/4/f/dataset_64f0eb5c-7696-44cb-af7f-1fb99383107f.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:34:21,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (34) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/34/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/34/galaxy_34.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 34 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:21,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 34 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:22,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:22,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:32,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4g76w with k8s id: gxy-4g76w succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:34:32,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 33: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:33,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-gj79l with k8s id: gxy-gj79l succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:33,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-c6xwb with k8s id: gxy-c6xwb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:34:33,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 35: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:34:33,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 34: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:34:45,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2024-10-05 06:34:45,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.jobs INFO 2024-10-05 06:34:45,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2024-10-05 06:34:45,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 33 executed (119.532 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:45,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 33 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:34:46,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 34 finished +galaxy.model.metadata DEBUG 2024-10-05 06:34:46,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.jobs INFO 2024-10-05 06:34:46,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 34 in /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs DEBUG 2024-10-05 06:34:46,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 34 executed (92.895 ms) +galaxy.jobs.runners DEBUG 2024-10-05 06:34:46,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 35 finished +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:46,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 34 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-10-05 06:34:47,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.jobs INFO 2024-10-05 06:34:47,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 35 in /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs DEBUG 2024-10-05 06:34:47,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 35 executed (97.778 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:47,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 35 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:34:47,517 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 36 +tpv.core.entities DEBUG 2024-10-05 06:34:47,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:34:47,552 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:34:47,556 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:34:47,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:34:47,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Working directory for job is: /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs.runners DEBUG 2024-10-05 06:34:47,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [36] queued (40.600 ms) +galaxy.jobs.handler INFO 2024-10-05 06:34:47,599 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:47,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 36 +galaxy.jobs DEBUG 2024-10-05 06:34:47,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [36] prepared (60.224 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:47,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:34:47,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:47,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:34:47,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/36/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/3/f/f/dataset_3ffddad1-502f-4a96-970a-31846931e9e1.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/6/4/f/dataset_64f0eb5c-7696-44cb-af7f-1fb99383107f.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='CCCCCCNNNNNNNNNN' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/b/d/2/dataset_bd2e62e9-a9f3-4f7e-96c2-91a40ac6e155.dat' False --log='/galaxy/server/database/objects/4/b/d/dataset_4bda4bf3-512e-4247-8559-f2614f84a964.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/3/6/8/dataset_368970bf-e55b-465f-97e4-a73dff95885c.dat' && mv out2.gz '/galaxy/server/database/objects/0/2/e/dataset_02e3e0a1-1cdb-4a3e-85f2-c96a7538da58.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:34:47,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (36) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/36/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/36/galaxy_36.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:47,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 36 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:47,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:34:47,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:34:47,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:47,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 36 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:48,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:34:54,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-r72cf with k8s id: gxy-r72cf succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:34:54,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 36: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:35:03,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 36 finished +galaxy.model.metadata DEBUG 2024-10-05 06:35:03,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.model.metadata DEBUG 2024-10-05 06:35:03,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.model.metadata DEBUG 2024-10-05 06:35:03,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.util WARNING 2024-10-05 06:35:03,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/6/8/dataset_368970bf-e55b-465f-97e4-a73dff95885c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/6/8/dataset_368970bf-e55b-465f-97e4-a73dff95885c.dat' +galaxy.util WARNING 2024-10-05 06:35:03,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/0/2/e/dataset_02e3e0a1-1cdb-4a3e-85f2-c96a7538da58.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/0/2/e/dataset_02e3e0a1-1cdb-4a3e-85f2-c96a7538da58.dat' +galaxy.jobs INFO 2024-10-05 06:35:03,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs DEBUG 2024-10-05 06:35:03,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 36 executed (95.121 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:03,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 36 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:35:05,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 37, 39, 38 +tpv.core.entities DEBUG 2024-10-05 06:35:05,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:35:05,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:35:05,982 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:35:05,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:35:06,008 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Working directory for job is: /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:06,016 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [37] queued (33.647 ms) +galaxy.jobs.handler INFO 2024-10-05 06:35:06,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 37 +tpv.core.entities DEBUG 2024-10-05 06:35:06,032 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:35:06,032 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:35:06,036 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:35:06,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:35:06,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Working directory for job is: /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:06,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [39] queued (46.486 ms) +galaxy.jobs.handler INFO 2024-10-05 06:35:06,085 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 39 +tpv.core.entities DEBUG 2024-10-05 06:35:06,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:35:06,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:35:06,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:35:06,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:35:06,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [37] prepared (108.912 ms) +galaxy.jobs DEBUG 2024-10-05 06:35:06,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Working directory for job is: /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:06,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [38] queued (58.727 ms) +galaxy.jobs.handler INFO 2024-10-05 06:35:06,170 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.command_factory INFO 2024-10-05 06:35:06,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/37/registry.xml' '/galaxy/server/database/jobs_directory/000/37/upload_params.json' '52:/galaxy/server/database/objects/9/6/d/dataset_96d0e81d-cd8f-4de7-b561-263952667561_files:/galaxy/server/database/objects/9/6/d/dataset_96d0e81d-cd8f-4de7-b561-263952667561.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 38 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:06,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (37) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/37/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/37/galaxy_37.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 37 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:35:06,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [39] prepared (104.730 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 37 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:35:06,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '54:/galaxy/server/database/objects/8/4/c/dataset_84c11834-1bc3-46e5-8f36-8cc099aa9c88_files:/galaxy/server/database/objects/8/4/c/dataset_84c11834-1bc3-46e5-8f36-8cc099aa9c88.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:35:06,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (39) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/39/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/39/galaxy_39.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:35:06,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [38] prepared (91.160 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 39 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:35:06,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/38/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/38/registry.xml' '/galaxy/server/database/jobs_directory/000/38/upload_params.json' '53:/galaxy/server/database/objects/a/3/4/dataset_a34386c7-e30f-496f-8ea3-4b355ae8d82c_files:/galaxy/server/database/objects/a/3/4/dataset_a34386c7-e30f-496f-8ea3-4b355ae8d82c.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:35:06,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (38) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/38/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/38/galaxy_38.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 39 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 38 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:06,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 38 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:07,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:07,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:07,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:18,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zt96k with k8s id: gxy-zt96k succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:18,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-86dnm with k8s id: gxy-86dnm succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:35:18,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 37: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:35:18,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 38: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:19,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9k4x7 with k8s id: gxy-9k4x7 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:35:19,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 39: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:35:32,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 37 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:35:32,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2024-10-05 06:35:32,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.model.metadata DEBUG 2024-10-05 06:35:32,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.jobs INFO 2024-10-05 06:35:32,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 37 in /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs INFO 2024-10-05 06:35:32,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs DEBUG 2024-10-05 06:35:32,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 37 executed (159.395 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:32,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 37 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:35:32,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 38 executed (125.266 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:32,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 38 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:35:33,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 39 finished +galaxy.model.metadata DEBUG 2024-10-05 06:35:33,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.jobs INFO 2024-10-05 06:35:33,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2024-10-05 06:35:33,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 39 executed (92.657 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:33,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 39 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:35:34,020 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 40 +tpv.core.entities DEBUG 2024-10-05 06:35:34,054 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:35:34,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:35:34,059 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:35:34,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:35:34,091 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Working directory for job is: /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:34,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [40] queued (40.953 ms) +galaxy.jobs.handler INFO 2024-10-05 06:35:34,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:34,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 40 +galaxy.jobs DEBUG 2024-10-05 06:35:34,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [40] prepared (61.934 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:35:34,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:35:34,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:35:34,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:35:34,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/40/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/6/d/dataset_96d0e81d-cd8f-4de7-b561-263952667561.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/a/3/4/dataset_a34386c7-e30f-496f-8ea3-4b355ae8d82c.dat' input_read2.gz && umi_tools extract --extract-method='regex' --bc-pattern='^(?P.{6})(?P.{10})' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/8/4/c/dataset_84c11834-1bc3-46e5-8f36-8cc099aa9c88.dat' False --log='/galaxy/server/database/objects/b/f/c/dataset_bfc2c131-0ec6-47fb-9705-f03773615f36.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/d/1/0/dataset_d10e7085-a1d1-455d-a244-3ee68ba05b85.dat' && mv out2.gz '/galaxy/server/database/objects/f/2/b/dataset_f2b56f81-4ce6-40c2-b2b7-ddf0c00d1fd5.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:35:34,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (40) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/40/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/40/galaxy_40.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:34,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 40 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:35:34,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:35:34,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:35:34,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:34,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 40 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:35,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:41,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j2n4t with k8s id: gxy-j2n4t succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:35:41,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:35:50,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2024-10-05 06:35:50,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.model.metadata DEBUG 2024-10-05 06:35:50,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.model.metadata DEBUG 2024-10-05 06:35:50,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.util WARNING 2024-10-05 06:35:50,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/d/1/0/dataset_d10e7085-a1d1-455d-a244-3ee68ba05b85.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/d/1/0/dataset_d10e7085-a1d1-455d-a244-3ee68ba05b85.dat' +galaxy.util WARNING 2024-10-05 06:35:50,518 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/2/b/dataset_f2b56f81-4ce6-40c2-b2b7-ddf0c00d1fd5.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/2/b/dataset_f2b56f81-4ce6-40c2-b2b7-ddf0c00d1fd5.dat' +galaxy.jobs INFO 2024-10-05 06:35:50,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 40 in /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs DEBUG 2024-10-05 06:35:50,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 40 executed (154.544 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:50,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 40 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:35:52,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 41, 42 +tpv.core.entities DEBUG 2024-10-05 06:35:52,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:35:52,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:35:52,488 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:35:52,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:35:52,512 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Working directory for job is: /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:52,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [41] queued (38.262 ms) +galaxy.jobs.handler INFO 2024-10-05 06:35:52,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:52,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 41 +tpv.core.entities DEBUG 2024-10-05 06:35:52,541 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:35:52,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:35:52,546 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:35:52,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:35:52,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Working directory for job is: /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs.runners DEBUG 2024-10-05 06:35:52,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [42] queued (49.484 ms) +galaxy.jobs.handler INFO 2024-10-05 06:35:52,598 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:52,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 42 +galaxy.jobs DEBUG 2024-10-05 06:35:52,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [41] prepared (97.190 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:35:52,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/41/registry.xml' '/galaxy/server/database/jobs_directory/000/41/upload_params.json' '58:/galaxy/server/database/objects/d/f/8/dataset_df88a6ab-3eee-4161-9276-425ab70f26d3_files:/galaxy/server/database/objects/d/f/8/dataset_df88a6ab-3eee-4161-9276-425ab70f26d3.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:35:52,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (41) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/41/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/41/galaxy_41.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:35:52,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [42] prepared (82.603 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:52,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:52,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:35:52,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/42/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/42/registry.xml' '/galaxy/server/database/jobs_directory/000/42/upload_params.json' '59:/galaxy/server/database/objects/d/c/d/dataset_dcd26eea-8bb3-4ca7-a47d-2a1e7816c8ca_files:/galaxy/server/database/objects/d/c/d/dataset_dcd26eea-8bb3-4ca7-a47d-2a1e7816c8ca.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:35:52,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (42) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/42/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/42/galaxy_42.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:52,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 42 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:52,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 42 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:53,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:35:53,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:03,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rgds4 with k8s id: gxy-rgds4 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:03,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-p6b54 with k8s id: gxy-p6b54 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:36:03,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 41: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:36:03,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 42: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:36:13,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 41 finished +galaxy.model.metadata DEBUG 2024-10-05 06:36:13,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.jobs.runners DEBUG 2024-10-05 06:36:13,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 42 finished +galaxy.jobs INFO 2024-10-05 06:36:13,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 41 in /galaxy/server/database/jobs_directory/000/41 +galaxy.model.metadata DEBUG 2024-10-05 06:36:13,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs DEBUG 2024-10-05 06:36:13,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 41 executed (119.624 ms) +galaxy.jobs INFO 2024-10-05 06:36:13,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 42 in /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:13,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:36:13,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 42 executed (100.055 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:13,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 42 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:36:14,020 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 43 +tpv.core.entities DEBUG 2024-10-05 06:36:14,053 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:36:14,054 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:36:14,058 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:36:14,070 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:36:14,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Working directory for job is: /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs.runners DEBUG 2024-10-05 06:36:14,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [43] queued (40.740 ms) +galaxy.jobs.handler INFO 2024-10-05 06:36:14,101 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:14,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 43 +galaxy.jobs DEBUG 2024-10-05 06:36:14,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [43] prepared (55.037 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:14,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:36:14,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:14,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:36:14,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/d/f/8/dataset_df88a6ab-3eee-4161-9276-425ab70f26d3.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/d/c/d/dataset_dcd26eea-8bb3-4ca7-a47d-2a1e7816c8ca.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/0/5/d/dataset_05ddf729-db3a-49a3-855f-4977775dacab.dat' && mv out2.gz '/galaxy/server/database/objects/6/3/e/dataset_63e9bcca-69e2-48ea-8ae7-9e70360eb30a.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:36:14,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (43) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/43/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/43/galaxy_43.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:14,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 43 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:14,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:36:14,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:14,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:14,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 43 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:14,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:20,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5hdm7 with k8s id: gxy-5hdm7 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:36:20,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 43: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:36:29,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2024-10-05 06:36:29,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.model.metadata DEBUG 2024-10-05 06:36:29,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.util WARNING 2024-10-05 06:36:29,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/0/5/d/dataset_05ddf729-db3a-49a3-855f-4977775dacab.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/0/5/d/dataset_05ddf729-db3a-49a3-855f-4977775dacab.dat' +galaxy.util WARNING 2024-10-05 06:36:29,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/3/e/dataset_63e9bcca-69e2-48ea-8ae7-9e70360eb30a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/3/e/dataset_63e9bcca-69e2-48ea-8ae7-9e70360eb30a.dat' +galaxy.jobs INFO 2024-10-05 06:36:29,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 43 in /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs DEBUG 2024-10-05 06:36:29,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 43 executed (81.185 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:30,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 43 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:36:32,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 44 +tpv.core.entities DEBUG 2024-10-05 06:36:32,487 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:36:32,487 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:36:32,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:36:32,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:36:32,518 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Working directory for job is: /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs.runners DEBUG 2024-10-05 06:36:32,525 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [44] queued (33.743 ms) +galaxy.jobs.handler INFO 2024-10-05 06:36:32,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:32,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 44 +galaxy.jobs DEBUG 2024-10-05 06:36:32,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [44] prepared (78.143 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:36:32,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/44/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/44/registry.xml' '/galaxy/server/database/jobs_directory/000/44/upload_params.json' '62:/galaxy/server/database/objects/8/a/a/dataset_8aa5937c-a544-4b39-9ab4-5a156eb9767c_files:/galaxy/server/database/objects/8/a/a/dataset_8aa5937c-a544-4b39-9ab4-5a156eb9767c.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:36:32,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (44) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/44/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/44/galaxy_44.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:32,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 44 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:32,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 44 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:32,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:43,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-lkqsl with k8s id: gxy-lkqsl succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:36:44,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 44: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:36:53,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 44 finished +galaxy.model.metadata DEBUG 2024-10-05 06:36:53,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 62 +galaxy.jobs INFO 2024-10-05 06:36:53,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2024-10-05 06:36:53,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 44 executed (85.129 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:53,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 44 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:36:53,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 45 +tpv.core.entities DEBUG 2024-10-05 06:36:53,968 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:36:53,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:36:53,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:36:53,983 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:36:54,000 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Working directory for job is: /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs.runners DEBUG 2024-10-05 06:36:54,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [45] queued (35.938 ms) +galaxy.jobs.handler INFO 2024-10-05 06:36:54,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:54,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 45 +galaxy.jobs DEBUG 2024-10-05 06:36:54,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [45] prepared (49.577 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:54,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:36:54,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:54,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:36:54,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/8/a/a/dataset_8aa5937c-a544-4b39-9ab4-5a156eb9767c.dat' input_single.txt && umi_tools extract --extract-method='string' --bc-pattern='XXXNNN' --3prime --stdin=input_single.txt --stdout '/galaxy/server/database/objects/1/2/6/dataset_1261f68e-c8bb-4df5-982c-164b25b80d1a.dat' False --quality-filter-threshold '10' --quality-encoding phred33 --log='/galaxy/server/database/objects/6/7/6/dataset_676ca616-7a90-479b-b2dd-78a2271c1469.dat' --log2stderr] +galaxy.jobs.runners DEBUG 2024-10-05 06:36:54,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (45) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/45/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/45/galaxy_45.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:54,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 45 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:54,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:36:54,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:36:54,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:54,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 45 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:36:55,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:00,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kqr66 with k8s id: gxy-kqr66 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:37:00,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 45: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:37:09,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 45 finished +galaxy.model.metadata DEBUG 2024-10-05 06:37:09,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.model.metadata DEBUG 2024-10-05 06:37:09,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2024-10-05 06:37:09,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs DEBUG 2024-10-05 06:37:09,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 45 executed (83.941 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:09,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 45 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:37:11,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 46, 47 +tpv.core.entities DEBUG 2024-10-05 06:37:11,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:37:11,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:37:11,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:37:11,385 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:37:11,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Working directory for job is: /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs.runners DEBUG 2024-10-05 06:37:11,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [46] queued (32.922 ms) +galaxy.jobs.handler INFO 2024-10-05 06:37:11,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:11,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 46 +tpv.core.entities DEBUG 2024-10-05 06:37:11,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:37:11,420 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:37:11,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:37:11,436 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:37:11,463 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Working directory for job is: /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs.runners DEBUG 2024-10-05 06:37:11,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [47] queued (46.972 ms) +galaxy.jobs.handler INFO 2024-10-05 06:37:11,473 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:11,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 47 +galaxy.jobs DEBUG 2024-10-05 06:37:11,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [46] prepared (99.810 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:37:11,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/46/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/46/registry.xml' '/galaxy/server/database/jobs_directory/000/46/upload_params.json' '65:/galaxy/server/database/objects/d/7/1/dataset_d7146e12-5f11-4fea-acdb-1e2073a44b70_files:/galaxy/server/database/objects/d/7/1/dataset_d7146e12-5f11-4fea-acdb-1e2073a44b70.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:37:11,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (46) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/46/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/46/galaxy_46.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:37:11,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [47] prepared (81.544 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:11,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 46 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:11,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 46 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:37:11,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/47/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/47/registry.xml' '/galaxy/server/database/jobs_directory/000/47/upload_params.json' '66:/galaxy/server/database/objects/2/f/1/dataset_2f1af5da-593d-42fc-9b9b-02c9dd00d6ca_files:/galaxy/server/database/objects/2/f/1/dataset_2f1af5da-593d-42fc-9b9b-02c9dd00d6ca.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:37:11,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (47) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/47/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/47/galaxy_47.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:11,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 47 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:11,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 47 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:12,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:12,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:23,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2tsd8 with k8s id: gxy-2tsd8 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:23,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-44srl with k8s id: gxy-44srl succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:37:23,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 46: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:37:23,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 47: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:37:33,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 46 finished +galaxy.model.metadata DEBUG 2024-10-05 06:37:33,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2024-10-05 06:37:33,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 46 in /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs.runners DEBUG 2024-10-05 06:37:33,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 47 finished +galaxy.jobs DEBUG 2024-10-05 06:37:33,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 46 executed (104.514 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:33,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 46 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-10-05 06:37:33,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 66 +galaxy.jobs INFO 2024-10-05 06:37:33,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 47 in /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs DEBUG 2024-10-05 06:37:33,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 47 executed (107.217 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:33,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 47 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:37:34,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 48 +tpv.core.entities DEBUG 2024-10-05 06:37:34,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:37:34,061 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:37:34,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:37:34,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:37:34,094 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Working directory for job is: /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs.runners DEBUG 2024-10-05 06:37:34,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [48] queued (38.084 ms) +galaxy.jobs.handler INFO 2024-10-05 06:37:34,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:34,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 48 +galaxy.jobs DEBUG 2024-10-05 06:37:34,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [48] prepared (58.786 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:37:34,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:37:34,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:37:34,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:37:34,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/48/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/d/7/1/dataset_d7146e12-5f11-4fea-acdb-1e2073a44b70.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/2/f/1/dataset_2f1af5da-593d-42fc-9b9b-02c9dd00d6ca.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log='/galaxy/server/database/objects/9/7/6/dataset_97690e6b-dd41-49fa-ad63-ca2865ecc9c6.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/6/7/2/dataset_672dc685-1749-4cd0-b302-469c777296c7.dat' && mv out2.gz '/galaxy/server/database/objects/4/4/d/dataset_44d685b4-b6e3-4f79-bef8-d2db068a1333.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:37:34,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (48) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/48/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/48/galaxy_48.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:34,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 48 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:37:34,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:37:34,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:37:34,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:34,515 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 48 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:35,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:41,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ljw9b with k8s id: gxy-ljw9b succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:37:41,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 48: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:37:50,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 48 finished +galaxy.model.metadata DEBUG 2024-10-05 06:37:50,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 69 +galaxy.model.metadata DEBUG 2024-10-05 06:37:50,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 67 +galaxy.model.metadata DEBUG 2024-10-05 06:37:50,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 68 +galaxy.util WARNING 2024-10-05 06:37:50,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/7/2/dataset_672dc685-1749-4cd0-b302-469c777296c7.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/7/2/dataset_672dc685-1749-4cd0-b302-469c777296c7.dat' +galaxy.util WARNING 2024-10-05 06:37:50,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/4/d/dataset_44d685b4-b6e3-4f79-bef8-d2db068a1333.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/4/d/dataset_44d685b4-b6e3-4f79-bef8-d2db068a1333.dat' +galaxy.jobs INFO 2024-10-05 06:37:50,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs DEBUG 2024-10-05 06:37:50,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 48 executed (96.040 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:50,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 48 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:37:53,510 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 50, 49 +tpv.core.entities DEBUG 2024-10-05 06:37:53,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:37:53,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:37:53,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:37:53,554 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:37:53,568 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Working directory for job is: /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs.runners DEBUG 2024-10-05 06:37:53,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [49] queued (33.760 ms) +galaxy.jobs.handler INFO 2024-10-05 06:37:53,578 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:53,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 49 +tpv.core.entities DEBUG 2024-10-05 06:37:53,589 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:37:53,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:37:53,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:37:53,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:37:53,636 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Working directory for job is: /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs.runners DEBUG 2024-10-05 06:37:53,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [50] queued (49.454 ms) +galaxy.jobs.handler INFO 2024-10-05 06:37:53,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:53,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 50 +galaxy.jobs DEBUG 2024-10-05 06:37:53,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [49] prepared (87.786 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:37:53,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/49/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/49/registry.xml' '/galaxy/server/database/jobs_directory/000/49/upload_params.json' '70:/galaxy/server/database/objects/6/0/d/dataset_60d6d110-d7a5-400b-8a23-24853588f2a8_files:/galaxy/server/database/objects/6/0/d/dataset_60d6d110-d7a5-400b-8a23-24853588f2a8.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:37:53,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (49) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/49/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/49/galaxy_49.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:53,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 49 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:37:53,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [50] prepared (82.613 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:53,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 49 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:37:53,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/50/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/50/registry.xml' '/galaxy/server/database/jobs_directory/000/50/upload_params.json' '71:/galaxy/server/database/objects/3/7/b/dataset_37b191af-99dd-4784-ab03-f7cc2d427bc8_files:/galaxy/server/database/objects/3/7/b/dataset_37b191af-99dd-4784-ab03-f7cc2d427bc8.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:37:53,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (50) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/50/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/50/galaxy_50.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:53,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 50 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:53,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 50 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:54,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:37:54,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:05,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-d99jh with k8s id: gxy-d99jh succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:05,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hdv2k with k8s id: gxy-hdv2k succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:38:05,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 49: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:38:05,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:38:14,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 50 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:38:14,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 49 finished +galaxy.model.metadata DEBUG 2024-10-05 06:38:14,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 71 +galaxy.jobs INFO 2024-10-05 06:38:14,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 50 in /galaxy/server/database/jobs_directory/000/50 +galaxy.model.metadata DEBUG 2024-10-05 06:38:14,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 70 +galaxy.jobs INFO 2024-10-05 06:38:14,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 49 in /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs DEBUG 2024-10-05 06:38:14,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 50 executed (130.838 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:14,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 50 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:38:14,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 49 executed (118.842 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:14,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 49 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:38:16,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 51 +tpv.core.entities DEBUG 2024-10-05 06:38:16,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:38:16,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:38:16,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:38:16,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:38:16,142 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Working directory for job is: /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs.runners DEBUG 2024-10-05 06:38:16,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [51] queued (39.580 ms) +galaxy.jobs.handler INFO 2024-10-05 06:38:16,153 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:16,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 51 +galaxy.tools.evaluation INFO 2024-10-05 06:38:16,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Updating param_dict for forward with /galaxy/server/database/objects/1/c/2/dataset_1c26808d-8eda-404b-b3cf-d1fb784a89e3.dat +galaxy.tools.evaluation INFO 2024-10-05 06:38:16,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Updating param_dict for reverse with /galaxy/server/database/objects/7/c/1/dataset_7c1ab5c6-ca32-42b6-9134-837101ed5ada.dat +galaxy.jobs DEBUG 2024-10-05 06:38:16,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [51] prepared (68.461 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:38:16,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:38:16,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:38:16,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:38:16,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/6/0/d/dataset_60d6d110-d7a5-400b-8a23-24853588f2a8.dat' input_read1.txt && ln -s '/galaxy/server/database/objects/3/7/b/dataset_37b191af-99dd-4784-ab03-f7cc2d427bc8.dat' input_read2.txt && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.txt --read2-in=input_read2.txt --stdout '/galaxy/server/database/objects/1/c/2/dataset_1c26808d-8eda-404b-b3cf-d1fb784a89e3.dat' --read2-out='/galaxy/server/database/objects/7/c/1/dataset_7c1ab5c6-ca32-42b6-9134-837101ed5ada.dat' False --log='/galaxy/server/database/objects/6/f/4/dataset_6f4d1c97-5b9e-4e3b-bae2-70ca4b027418.dat' --log2stderr] +galaxy.jobs.runners DEBUG 2024-10-05 06:38:16,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (51) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/51/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/51/galaxy_51.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:16,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 51 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:38:16,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:38:16,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:38:16,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:16,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 51 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:17,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:22,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-mbhlc with k8s id: gxy-mbhlc succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:38:22,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 51: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:38:31,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 51 finished +galaxy.model.metadata DEBUG 2024-10-05 06:38:31,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 73 +galaxy.model.metadata DEBUG 2024-10-05 06:38:31,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 72 +galaxy.model.metadata DEBUG 2024-10-05 06:38:31,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 74 +galaxy.jobs INFO 2024-10-05 06:38:31,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 51 in /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs DEBUG 2024-10-05 06:38:31,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 51 executed (118.683 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:31,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 51 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:38:33,525 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52, 53 +tpv.core.entities DEBUG 2024-10-05 06:38:33,552 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:38:33,553 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:38:33,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:38:33,568 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:38:33,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Working directory for job is: /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs.runners DEBUG 2024-10-05 06:38:33,588 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [52] queued (30.705 ms) +galaxy.jobs.handler INFO 2024-10-05 06:38:33,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:33,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 52 +tpv.core.entities DEBUG 2024-10-05 06:38:33,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:38:33,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:38:33,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:38:33,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:38:33,646 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Working directory for job is: /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs.runners DEBUG 2024-10-05 06:38:33,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [53] queued (48.303 ms) +galaxy.jobs.handler INFO 2024-10-05 06:38:33,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:33,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 53 +galaxy.jobs DEBUG 2024-10-05 06:38:33,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [52] prepared (95.332 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:38:33,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/52/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/52/registry.xml' '/galaxy/server/database/jobs_directory/000/52/upload_params.json' '75:/galaxy/server/database/objects/9/0/5/dataset_9050a585-8a74-41a8-9213-a845d72b8a4b_files:/galaxy/server/database/objects/9/0/5/dataset_9050a585-8a74-41a8-9213-a845d72b8a4b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:38:33,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (52) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/52/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/52/galaxy_52.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:38:33,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [53] prepared (77.865 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:33,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 52 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:33,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 52 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:38:33,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/53/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/53/registry.xml' '/galaxy/server/database/jobs_directory/000/53/upload_params.json' '76:/galaxy/server/database/objects/0/e/7/dataset_0e75abdf-ef93-4d07-a77a-6d9a90d7af68_files:/galaxy/server/database/objects/0/e/7/dataset_0e75abdf-ef93-4d07-a77a-6d9a90d7af68.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:38:33,780 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (53) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/53/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/53/galaxy_53.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:33,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 53 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:33,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 53 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:34,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:34,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:38:34,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 54 +tpv.core.entities DEBUG 2024-10-05 06:38:34,698 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:38:34,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:38:34,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:38:34,715 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:38:34,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Working directory for job is: /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs.runners DEBUG 2024-10-05 06:38:34,737 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [54] queued (34.464 ms) +galaxy.jobs.handler INFO 2024-10-05 06:38:34,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:34,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 54 +galaxy.jobs DEBUG 2024-10-05 06:38:34,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [54] prepared (74.411 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:38:34,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/54/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/54/registry.xml' '/galaxy/server/database/jobs_directory/000/54/upload_params.json' '77:/galaxy/server/database/objects/f/3/d/dataset_f3dd47d3-ba44-41ec-9ce4-e6b17f0835e0_files:/galaxy/server/database/objects/f/3/d/dataset_f3dd47d3-ba44-41ec-9ce4-e6b17f0835e0.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:38:34,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (54) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/54/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/54/galaxy_54.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:34,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 54 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:34,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 54 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:35,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:45,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hxknv with k8s id: gxy-hxknv succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:45,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-w8rgb with k8s id: gxy-w8rgb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:38:45,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 52: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:38:45,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 53: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:46,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-t52gm with k8s id: gxy-t52gm succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:38:46,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 54: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:38:59,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 52 finished +galaxy.model.metadata DEBUG 2024-10-05 06:38:59,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 75 +galaxy.jobs INFO 2024-10-05 06:38:59,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 52 in /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs DEBUG 2024-10-05 06:38:59,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 52 executed (145.922 ms) +galaxy.jobs.runners DEBUG 2024-10-05 06:38:59,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 53 finished +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:59,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 52 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-10-05 06:38:59,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 76 +galaxy.jobs INFO 2024-10-05 06:38:59,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 53 in /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs DEBUG 2024-10-05 06:38:59,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 53 executed (103.278 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:38:59,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 53 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:00,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 54 finished +galaxy.model.metadata DEBUG 2024-10-05 06:39:00,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 77 +galaxy.jobs INFO 2024-10-05 06:39:00,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 54 in /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs DEBUG 2024-10-05 06:39:00,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 54 executed (96.419 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:00,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 54 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:39:01,496 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 55 +tpv.core.entities DEBUG 2024-10-05 06:39:01,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:01,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:01,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:01,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:01,568 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Working directory for job is: /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:01,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [55] queued (41.499 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:01,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:01,584 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 55 +galaxy.jobs DEBUG 2024-10-05 06:39:01,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [55] prepared (58.845 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:01,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:39:01,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:01,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:39:01,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/9/0/5/dataset_9050a585-8a74-41a8-9213-a845d72b8a4b.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/0/e/7/dataset_0e75abdf-ef93-4d07-a77a-6d9a90d7af68.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='CCCCCCNNNNNNNNNN' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/f/3/d/dataset_f3dd47d3-ba44-41ec-9ce4-e6b17f0835e0.dat' False --log='/galaxy/server/database/objects/4/7/d/dataset_47d28eae-9b16-4d6b-9324-42de7593b94e.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/5/b/0/dataset_5b0e5b07-26f7-4cd1-b6b9-f4af1b4a8c0d.dat' && mv out2.gz '/galaxy/server/database/objects/c/2/8/dataset_c288a374-62c3-404b-a1fd-f562537dc804.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:01,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (55) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/55/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/55/galaxy_55.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:01,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:01,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:39:01,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:01,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:01,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:02,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-fkj9h failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-fkj9h. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:39:07,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-fkj9h + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-fkj9h": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (55/gxy-fkj9h) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (55/gxy-fkj9h) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (55/gxy-fkj9h) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (55/gxy-fkj9h) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-fkj9h. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Attempting to stop job 55 (gxy-fkj9h) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Found job with id gxy-fkj9h to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:07,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:08,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (55/gxy-fkj9h) Terminated at user's request +galaxy.util WARNING 2024-10-05 06:39:08,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/b/0/dataset_5b0e5b07-26f7-4cd1-b6b9-f4af1b4a8c0d.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/b/0/dataset_5b0e5b07-26f7-4cd1-b6b9-f4af1b4a8c0d.dat' +galaxy.util WARNING 2024-10-05 06:39:08,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/2/8/dataset_c288a374-62c3-404b-a1fd-f562537dc804.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/2/8/dataset_c288a374-62c3-404b-a1fd-f562537dc804.dat' +galaxy.jobs.handler DEBUG 2024-10-05 06:39:09,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 56, 58, 57 +tpv.core.entities DEBUG 2024-10-05 06:39:09,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:09,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:09,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:09,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:09,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Working directory for job is: /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:09,784 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [56] queued (33.329 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:09,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:09,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 56 +tpv.core.entities DEBUG 2024-10-05 06:39:09,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:09,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:09,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:09,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:09,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Working directory for job is: /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:09,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [57] queued (45.302 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:09,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:09,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 57 +tpv.core.entities DEBUG 2024-10-05 06:39:09,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:09,868 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:09,872 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:09,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:09,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [56] prepared (102.470 ms) +galaxy.jobs DEBUG 2024-10-05 06:39:09,921 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Working directory for job is: /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:09,930 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [58] queued (57.923 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:09,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.command_factory INFO 2024-10-05 06:39:09,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/56/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/56/registry.xml' '/galaxy/server/database/jobs_directory/000/56/upload_params.json' '81:/galaxy/server/database/objects/6/0/b/dataset_60b8daa2-0b9f-4bc0-9c21-177dbebacf0f_files:/galaxy/server/database/objects/6/0/b/dataset_60b8daa2-0b9f-4bc0-9c21-177dbebacf0f.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:09,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 58 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:09,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (56) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/56/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/56/galaxy_56.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:39:09,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [57] prepared (119.515 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:09,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 56 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:39:10,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/57/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/57/registry.xml' '/galaxy/server/database/jobs_directory/000/57/upload_params.json' '82:/galaxy/server/database/objects/8/6/1/dataset_861e12e2-a95d-4d0d-af04-bc675de3c124_files:/galaxy/server/database/objects/8/6/1/dataset_861e12e2-a95d-4d0d-af04-bc675de3c124.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:10,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 56 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:10,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (57) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/57/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/57/galaxy_57.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:10,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 57 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:39:10,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [58] prepared (104.683 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:10,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 57 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:39:10,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/58/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/58/registry.xml' '/galaxy/server/database/jobs_directory/000/58/upload_params.json' '83:/galaxy/server/database/objects/7/8/3/dataset_783b4809-7fcf-40ca-8280-18d0c49404a2_files:/galaxy/server/database/objects/7/8/3/dataset_783b4809-7fcf-40ca-8280-18d0c49404a2.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:10,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (58) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/58/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/58/galaxy_58.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:10,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 58 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:10,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 58 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:10,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:11,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:11,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:21,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-c97jc with k8s id: gxy-c97jc succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:21,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qhtkm with k8s id: gxy-qhtkm succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:21,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qsbdw with k8s id: gxy-qsbdw succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:39:21,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 56: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:39:21,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:39:21,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:39:35,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 58 finished +galaxy.model.metadata DEBUG 2024-10-05 06:39:35,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:35,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 57 finished +galaxy.jobs INFO 2024-10-05 06:39:35,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 58 in /galaxy/server/database/jobs_directory/000/58 +galaxy.model.metadata DEBUG 2024-10-05 06:39:35,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.jobs DEBUG 2024-10-05 06:39:35,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 58 executed (156.908 ms) +galaxy.jobs.runners DEBUG 2024-10-05 06:39:35,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 56 finished +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:35,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 58 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs INFO 2024-10-05 06:39:35,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 57 in /galaxy/server/database/jobs_directory/000/57 +galaxy.model.metadata DEBUG 2024-10-05 06:39:35,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.jobs DEBUG 2024-10-05 06:39:35,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 57 executed (134.197 ms) +galaxy.jobs INFO 2024-10-05 06:39:35,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:35,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 57 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:39:35,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 56 executed (101.312 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:35,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 56 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:39:36,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 59 +tpv.core.entities DEBUG 2024-10-05 06:39:36,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:36,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:36,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:36,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:36,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Working directory for job is: /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:36,693 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [59] queued (37.199 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:36,695 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:36,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 59 +galaxy.jobs DEBUG 2024-10-05 06:39:36,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [59] prepared (57.378 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:36,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:39:36,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:36,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:39:36,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/6/0/b/dataset_60b8daa2-0b9f-4bc0-9c21-177dbebacf0f.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/8/6/1/dataset_861e12e2-a95d-4d0d-af04-bc675de3c124.dat' input_read2.gz && umi_tools extract --extract-method='regex' --bc-pattern='^(?P.{6})(?P.{10})' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/7/8/3/dataset_783b4809-7fcf-40ca-8280-18d0c49404a2.dat' False --log='/galaxy/server/database/objects/c/a/0/dataset_ca0ac285-a2c4-420c-8de5-37ed82492c6e.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/e/d/e/dataset_ede82578-dbc9-4368-9668-d80ca0f68d7a.dat' && mv out2.gz '/galaxy/server/database/objects/9/5/f/dataset_95f04cab-26f0-4c63-85dd-460d9d507578.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:36,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (59) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/59/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/59/galaxy_59.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:36,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 59 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:36,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:39:36,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:39:36,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:36,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 59 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:37,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:43,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wmrxq with k8s id: gxy-wmrxq succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:39:43,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:39:52,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2024-10-05 06:39:52,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.model.metadata DEBUG 2024-10-05 06:39:52,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.model.metadata DEBUG 2024-10-05 06:39:52,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.util WARNING 2024-10-05 06:39:53,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/d/e/dataset_ede82578-dbc9-4368-9668-d80ca0f68d7a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/d/e/dataset_ede82578-dbc9-4368-9668-d80ca0f68d7a.dat' +galaxy.util WARNING 2024-10-05 06:39:53,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/5/f/dataset_95f04cab-26f0-4c63-85dd-460d9d507578.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/5/f/dataset_95f04cab-26f0-4c63-85dd-460d9d507578.dat' +galaxy.jobs INFO 2024-10-05 06:39:53,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs DEBUG 2024-10-05 06:39:53,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 59 executed (102.589 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:53,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 59 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:39:54,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60 +tpv.core.entities DEBUG 2024-10-05 06:39:54,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:54,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:54,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:54,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:54,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Working directory for job is: /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:54,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [60] queued (33.916 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:54,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:54,286 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 60 +galaxy.jobs DEBUG 2024-10-05 06:39:54,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [60] prepared (76.533 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:39:54,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '87:/galaxy/server/database/objects/b/9/9/dataset_b99998c9-5079-466a-bd90-6b4ac47ef392_files:/galaxy/server/database/objects/b/9/9/dataset_b99998c9-5079-466a-bd90-6b4ac47ef392.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:54,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (60) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/60/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/60/galaxy_60.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:54,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 60 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:54,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 60 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:54,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:39:55,288 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2024-10-05 06:39:55,317 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:39:55,317 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:39:55,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:39:55,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:39:55,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Working directory for job is: /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs.runners DEBUG 2024-10-05 06:39:55,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [61] queued (34.981 ms) +galaxy.jobs.handler INFO 2024-10-05 06:39:55,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:55,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 61 +galaxy.jobs DEBUG 2024-10-05 06:39:55,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [61] prepared (77.493 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:39:55,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/61/registry.xml' '/galaxy/server/database/jobs_directory/000/61/upload_params.json' '88:/galaxy/server/database/objects/e/f/d/dataset_efd26cbf-3208-4678-be8b-be73c00f4356_files:/galaxy/server/database/objects/e/f/d/dataset_efd26cbf-3208-4678-be8b-be73c00f4356.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:39:55,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (61) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/61/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/61/galaxy_61.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:55,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 61 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:55,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 61 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:39:55,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:06,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vkgcz with k8s id: gxy-vkgcz succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:40:06,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 60: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:07,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-djbd7 with k8s id: gxy-djbd7 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:40:07,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 61: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:40:15,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 60 finished +galaxy.model.metadata DEBUG 2024-10-05 06:40:15,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.jobs INFO 2024-10-05 06:40:15,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs DEBUG 2024-10-05 06:40:15,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 60 executed (94.124 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:15,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 60 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:40:16,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 61 finished +galaxy.model.metadata DEBUG 2024-10-05 06:40:16,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 88 +galaxy.jobs INFO 2024-10-05 06:40:16,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 61 in /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs DEBUG 2024-10-05 06:40:16,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 61 executed (91.238 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:16,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 61 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:40:17,840 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62 +tpv.core.entities DEBUG 2024-10-05 06:40:17,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/.*, abstract=False, cores=1, mem=4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:40:17,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:40:17,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:40:17,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:40:17,903 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Working directory for job is: /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs.runners DEBUG 2024-10-05 06:40:17,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [62] queued (37.552 ms) +galaxy.jobs.handler INFO 2024-10-05 06:40:17,915 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:17,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 62 +galaxy.jobs DEBUG 2024-10-05 06:40:17,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [62] prepared (54.061 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:17,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:40:17,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:18,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:40:18,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/62/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/b/9/9/dataset_b99998c9-5079-466a-bd90-6b4ac47ef392.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/e/f/d/dataset_efd26cbf-3208-4678-be8b-be73c00f4356.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/5/1/b/dataset_51bc75bf-3db8-4f22-9b83-0177410c5511.dat' && mv out2.gz '/galaxy/server/database/objects/c/8/5/dataset_c850d4a7-42a1-430b-81e0-4ea7da635e32.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:40:18,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/62/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/62/galaxy_62.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:18,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:18,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:40:18,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2: umi_tools:1.1.2 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:18,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/umi_tools:1.1.2--py310h1425a21_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:18,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:19,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7nbzx failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-7nbzx. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:40:23,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-7nbzx + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-7nbzx": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62/gxy-7nbzx) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62/gxy-7nbzx) tool_stderr: # UMI-tools version: 1.1.2 +# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr +# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794 +# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64 +# blacklist : None +# compresslevel : 6 +# correct_umi_threshold : 0 +# either_read : False +# either_read_resolve : discard +# error_correct_cell : False +# extract_method : string +# filter_cell_barcode : None +# filter_cell_barcodes : False +# filter_umi : None +# filtered_out : None +# filtered_out2 : None +# ignore_suffix : False +# log2stderr : True +# loglevel : 1 +# pattern : NNNNNNCCCCCC +# pattern2 : None +# prime3 : None +# quality_encoding : None +# quality_filter_mask : None +# quality_filter_threshold : None +# random_seed : None +# read2_in : input_read2.gz +# read2_out : out2.gz +# read2_stdout : False +# reads_subset : None +# reconcile : False +# retain_umi : None +# short_help : None +# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> +# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> +# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> +# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +# tmpdir : None +# umi_correct_log : None +# umi_whitelist : None +# umi_whitelist_paired : None +# whitelist : None +2024-10-05 06:40:20,721 INFO Starting barcode extraction +2024-10-05 06:40:20,728 INFO Input Reads: 50 +2024-10-05 06:40:20,729 INFO Reads output: 50 +# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794 + +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62/gxy-7nbzx) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62/gxy-7nbzx) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-7nbzx. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 62 (gxy-7nbzx) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-7nbzx to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:23,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62/gxy-7nbzx) Terminated at user's request +galaxy.util WARNING 2024-10-05 06:40:23,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/1/b/dataset_51bc75bf-3db8-4f22-9b83-0177410c5511.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/1/b/dataset_51bc75bf-3db8-4f22-9b83-0177410c5511.dat' +galaxy.util WARNING 2024-10-05 06:40:23,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/8/5/dataset_c850d4a7-42a1-430b-81e0-4ea7da635e32.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/8/5/dataset_c850d4a7-42a1-430b-81e0-4ea7da635e32.dat' +galaxy.jobs.handler DEBUG 2024-10-05 06:40:26,059 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64, 63 +tpv.core.entities DEBUG 2024-10-05 06:40:26,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:40:26,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:40:26,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:40:26,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:40:26,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Working directory for job is: /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs.runners DEBUG 2024-10-05 06:40:26,130 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [63] queued (37.058 ms) +galaxy.jobs.handler INFO 2024-10-05 06:40:26,133 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:26,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 63 +tpv.core.entities DEBUG 2024-10-05 06:40:26,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:40:26,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:40:26,150 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:40:26,163 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:40:26,187 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Working directory for job is: /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs.runners DEBUG 2024-10-05 06:40:26,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [64] queued (44.397 ms) +galaxy.jobs.handler INFO 2024-10-05 06:40:26,197 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:26,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 64 +galaxy.jobs DEBUG 2024-10-05 06:40:26,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [63] prepared (104.839 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:40:26,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/63/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/63/registry.xml' '/galaxy/server/database/jobs_directory/000/63/upload_params.json' '91:/galaxy/server/database/objects/8/3/7/dataset_837dc26e-1024-4181-bc1a-658376dde6c4_files:/galaxy/server/database/objects/8/3/7/dataset_837dc26e-1024-4181-bc1a-658376dde6c4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:40:26,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (63) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/63/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/63/galaxy_63.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:40:26,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [64] prepared (82.933 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:26,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 63 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:26,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 63 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:40:26,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/64/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/64/registry.xml' '/galaxy/server/database/jobs_directory/000/64/upload_params.json' '92:/galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e_files:/galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:40:26,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (64) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/64/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/64/galaxy_64.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:26,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 64 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:26,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 64 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:27,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:27,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:37,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vpqmr with k8s id: gxy-vpqmr succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:37,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tj7fc with k8s id: gxy-tj7fc succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:40:38,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 63: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:40:38,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:40:47,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2024-10-05 06:40:47,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.jobs.runners DEBUG 2024-10-05 06:40:47,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 64 finished +galaxy.jobs INFO 2024-10-05 06:40:47,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 63 in /galaxy/server/database/jobs_directory/000/63 +galaxy.model.metadata DEBUG 2024-10-05 06:40:47,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.jobs DEBUG 2024-10-05 06:40:47,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 63 executed (135.887 ms) +galaxy.jobs INFO 2024-10-05 06:40:47,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 64 in /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:47,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 63 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:40:47,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 64 executed (105.350 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:47,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 64 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:40:48,725 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2024-10-05 06:40:48,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:40:48,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:40:48,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:40:48,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:40:48,786 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Working directory for job is: /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs.runners DEBUG 2024-10-05 06:40:48,795 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [65] queued (32.902 ms) +galaxy.jobs.handler INFO 2024-10-05 06:40:48,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:48,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 65 +cheetah_DynamicallyCompiledCheetahTemplate_1728110448_9082701_79619.py:119: SyntaxWarning: invalid escape sequence '\w' +galaxy.jobs DEBUG 2024-10-05 06:40:48,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [65] prepared (128.196 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:48,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:40:48,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:49,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:40:49,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/65/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/8/3/7/dataset_837dc26e-1024-4181-bc1a-658376dde6c4.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat' > first.sai && bwa samse 'localref.fa' first.sai '/galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/1/b/e/dataset_1be8f42d-946d-4a6f-92dd-40dfb355dba4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:40:49,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (65) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/65/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/65/galaxy_65.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:49,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 65 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:49,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:40:49,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:40:49,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:49,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 65 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:49,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:40:58,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j8cwt with k8s id: gxy-j8cwt succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:40:58,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:41:07,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2024-10-05 06:41:07,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.jobs INFO 2024-10-05 06:41:07,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 65 in /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs DEBUG 2024-10-05 06:41:07,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 65 executed (102.599 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:07,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 65 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:41:09,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67, 68, 66 +tpv.core.entities DEBUG 2024-10-05 06:41:09,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:09,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:09,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:09,235 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:09,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Working directory for job is: /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:09,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [66] queued (30.988 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:09,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 66 +tpv.core.entities DEBUG 2024-10-05 06:41:09,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:09,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:09,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:09,287 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:09,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Working directory for job is: /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:09,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [67] queued (49.733 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:09,326 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 67 +tpv.core.entities DEBUG 2024-10-05 06:41:09,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:09,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:09,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:09,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:09,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [66] prepared (107.112 ms) +galaxy.jobs DEBUG 2024-10-05 06:41:09,398 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Working directory for job is: /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:09,406 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [68] queued (56.295 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:09,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.command_factory INFO 2024-10-05 06:41:09,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/66/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '94:/galaxy/server/database/objects/5/2/d/dataset_52db4d9d-1352-4a9a-be6d-b2863b0d2e98_files:/galaxy/server/database/objects/5/2/d/dataset_52db4d9d-1352-4a9a-be6d-b2863b0d2e98.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 68 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:09,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (66) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/66/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/66/galaxy_66.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 66 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:41:09,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [67] prepared (95.247 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 66 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:41:09,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/67/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/67/registry.xml' '/galaxy/server/database/jobs_directory/000/67/upload_params.json' '95:/galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c_files:/galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:09,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (67) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/67/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/67/galaxy_67.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:41:09,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [68] prepared (93.397 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 67 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:41:09,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/68/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/68/registry.xml' '/galaxy/server/database/jobs_directory/000/68/upload_params.json' '96:/galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53_files:/galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:09,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (68) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/68/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/68/galaxy_68.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 67 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 68 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:09,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 68 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:10,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:10,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:10,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:21,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-z5mpg with k8s id: gxy-z5mpg succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:41:21,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:22,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-txrdt with k8s id: gxy-txrdt succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:22,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-nl698 with k8s id: gxy-nl698 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:41:22,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:41:22,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:41:34,694 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 66 finished +galaxy.model.metadata DEBUG 2024-10-05 06:41:34,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.jobs INFO 2024-10-05 06:41:34,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs DEBUG 2024-10-05 06:41:34,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 66 executed (133.641 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:34,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 66 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:35,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 67 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:41:35,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2024-10-05 06:41:36,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 95 +galaxy.model.metadata DEBUG 2024-10-05 06:41:36,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 96 +galaxy.jobs INFO 2024-10-05 06:41:36,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 67 in /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs INFO 2024-10-05 06:41:36,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 68 in /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs DEBUG 2024-10-05 06:41:36,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 67 executed (119.059 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:36,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 67 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:41:36,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 68 executed (116.554 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:36,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 68 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:41:37,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2024-10-05 06:41:37,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:37,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:37,299 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:37,311 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:37,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Working directory for job is: /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:37,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [69] queued (35.150 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:37,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:37,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 69 +galaxy.jobs DEBUG 2024-10-05 06:41:37,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [69] prepared (58.243 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:41:37,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:41:37,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:41:37,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:41:37,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/69/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/5/2/d/dataset_52db4d9d-1352-4a9a-be6d-b2863b0d2e98.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat' '/galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/1/b/8/dataset_1b8ef26f-453c-4fc7-bbd3-64c914cfd768.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:37,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (69) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/69/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/69/galaxy_69.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:37,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 69 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:41:37,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:41:37,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:41:37,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:37,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 69 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:38,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:42,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wl6c8 with k8s id: gxy-wl6c8 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:41:42,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:41:51,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2024-10-05 06:41:51,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 97 +galaxy.jobs INFO 2024-10-05 06:41:51,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2024-10-05 06:41:51,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 69 executed (112.806 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:51,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 69 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:41:52,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2024-10-05 06:41:52,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:52,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:52,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:52,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:52,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Working directory for job is: /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:52,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [70] queued (34.757 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:52,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:52,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 70 +galaxy.jobs DEBUG 2024-10-05 06:41:52,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [70] prepared (76.181 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:41:52,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/70/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/70/registry.xml' '/galaxy/server/database/jobs_directory/000/70/upload_params.json' '98:/galaxy/server/database/objects/c/6/8/dataset_c68c08a5-5eb9-4de5-8ebd-442bdccbbbf7_files:/galaxy/server/database/objects/c/6/8/dataset_c68c08a5-5eb9-4de5-8ebd-442bdccbbbf7.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:52,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (70) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/70/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/70/galaxy_70.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:52,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 70 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:52,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 70 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:53,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:41:53,804 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72, 71 +tpv.core.entities DEBUG 2024-10-05 06:41:53,831 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:53,831 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:53,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:53,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:53,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Working directory for job is: /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:53,868 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [71] queued (32.562 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:53,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:53,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 71 +tpv.core.entities DEBUG 2024-10-05 06:41:53,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:41:53,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:41:53,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:41:53,901 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:41:53,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Working directory for job is: /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs.runners DEBUG 2024-10-05 06:41:53,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [72] queued (49.144 ms) +galaxy.jobs.handler INFO 2024-10-05 06:41:53,940 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:53,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 72 +galaxy.jobs DEBUG 2024-10-05 06:41:53,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [71] prepared (99.473 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:41:54,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/71/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/71/registry.xml' '/galaxy/server/database/jobs_directory/000/71/upload_params.json' '99:/galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53_files:/galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:54,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (71) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/71/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/71/galaxy_71.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:54,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 71 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:41:54,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [72] prepared (85.715 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:54,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 71 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:41:54,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/72/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/72/registry.xml' '/galaxy/server/database/jobs_directory/000/72/upload_params.json' '100:/galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63_files:/galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:41:54,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (72) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/72/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/72/galaxy_72.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:54,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 72 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:54,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 72 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:54,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:41:54,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:03,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j5524 with k8s id: gxy-j5524 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:42:04,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 70: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:04,952 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dvrp2 with k8s id: gxy-dvrp2 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:04,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-shs97 with k8s id: gxy-shs97 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:42:05,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:42:05,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 72: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:42:17,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 70 finished +galaxy.model.metadata DEBUG 2024-10-05 06:42:18,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 98 +galaxy.jobs INFO 2024-10-05 06:42:18,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 70 in /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs DEBUG 2024-10-05 06:42:18,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 70 executed (119.102 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:18,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 70 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:42:18,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2024-10-05 06:42:19,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.jobs INFO 2024-10-05 06:42:19,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs.runners DEBUG 2024-10-05 06:42:19,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 72 finished +galaxy.jobs DEBUG 2024-10-05 06:42:19,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 71 executed (100.681 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:19,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 71 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-10-05 06:42:19,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs INFO 2024-10-05 06:42:19,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 72 in /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs DEBUG 2024-10-05 06:42:19,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 72 executed (102.561 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:19,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 72 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:42:19,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 73 +tpv.core.entities DEBUG 2024-10-05 06:42:19,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:42:19,649 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:42:19,653 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:42:19,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:42:19,678 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Working directory for job is: /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs.runners DEBUG 2024-10-05 06:42:19,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [73] queued (33.576 ms) +galaxy.jobs.handler INFO 2024-10-05 06:42:19,689 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:19,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 73 +galaxy.jobs DEBUG 2024-10-05 06:42:19,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [73] prepared (61.541 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:19,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:42:19,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:19,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:42:19,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/73/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/c/6/8/dataset_c68c08a5-5eb9-4de5-8ebd-442bdccbbbf7.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat' '/galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/2/0/e/dataset_20e76092-1b3b-405f-aa8d-b2349f597d98.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:42:19,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (73) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/73/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/73/galaxy_73.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:19,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 73 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:19,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:42:19,828 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:19,847 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:19,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 73 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:20,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:24,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j4m22 with k8s id: gxy-j4m22 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:42:24,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 73: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:42:33,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 73 finished +galaxy.model.metadata DEBUG 2024-10-05 06:42:33,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.jobs INFO 2024-10-05 06:42:33,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs DEBUG 2024-10-05 06:42:33,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 73 executed (108.737 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:33,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 73 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:42:34,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75, 74 +tpv.core.entities DEBUG 2024-10-05 06:42:35,001 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:42:35,001 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:42:35,007 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:42:35,020 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:42:35,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Working directory for job is: /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs.runners DEBUG 2024-10-05 06:42:35,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [74] queued (34.986 ms) +galaxy.jobs.handler INFO 2024-10-05 06:42:35,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:35,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 74 +tpv.core.entities DEBUG 2024-10-05 06:42:35,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:42:35,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:42:35,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:42:35,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:42:35,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Working directory for job is: /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs.runners DEBUG 2024-10-05 06:42:35,107 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [75] queued (46.145 ms) +galaxy.jobs.handler INFO 2024-10-05 06:42:35,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:35,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 75 +galaxy.jobs DEBUG 2024-10-05 06:42:35,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [74] prepared (98.127 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:42:35,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/74/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/74/registry.xml' '/galaxy/server/database/jobs_directory/000/74/upload_params.json' '102:/galaxy/server/database/objects/b/9/7/dataset_b979533e-58e2-4e94-8ec2-ee19d765c407_files:/galaxy/server/database/objects/b/9/7/dataset_b979533e-58e2-4e94-8ec2-ee19d765c407.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:42:35,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (74) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/74/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/74/galaxy_74.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:42:35,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [75] prepared (75.774 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:35,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 74 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:35,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 74 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:42:35,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/75/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '103:/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24_files:/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:42:35,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (75) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/75/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/75/galaxy_75.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:35,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 75 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:35,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 75 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:36,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:36,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:46,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tsm65 with k8s id: gxy-tsm65 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:42:46,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:47,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4ghvq with k8s id: gxy-4ghvq succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:42:47,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:42:56,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2024-10-05 06:42:56,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 102 +galaxy.jobs INFO 2024-10-05 06:42:56,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 74 in /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs DEBUG 2024-10-05 06:42:56,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 74 executed (111.454 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:56,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 74 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:42:57,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 75 finished +galaxy.model.metadata DEBUG 2024-10-05 06:42:57,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 103 +galaxy.jobs INFO 2024-10-05 06:42:57,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 75 in /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs DEBUG 2024-10-05 06:42:57,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 75 executed (98.918 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:57,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 75 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:42:58,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2024-10-05 06:42:58,642 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:42:58,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:42:58,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:42:58,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:42:58,672 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Working directory for job is: /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs.runners DEBUG 2024-10-05 06:42:58,681 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [76] queued (33.127 ms) +galaxy.jobs.handler INFO 2024-10-05 06:42:58,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:58,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 76 +galaxy.jobs DEBUG 2024-10-05 06:42:58,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [76] prepared (49.961 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:58,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:42:58,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:58,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:42:58,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/76/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/b/9/7/dataset_b979533e-58e2-4e94-8ec2-ee19d765c407.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" -b -1 'localref.fa' '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" -b -2 'localref.fa' '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/2/9/6/dataset_2969637e-0e3c-4114-b5ef-6a25d89da034.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:42:58,993 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (76) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/76/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/76/galaxy_76.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:59,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 76 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:59,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:42:59,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:42:59,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:59,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 76 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:42:59,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:03,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9rrhg with k8s id: gxy-9rrhg succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:43:03,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 76: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:43:13,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2024-10-05 06:43:13,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 104 +galaxy.jobs INFO 2024-10-05 06:43:13,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2024-10-05 06:43:13,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 76 executed (101.249 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:13,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 76 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:43:14,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79, 78, 77 +tpv.core.entities DEBUG 2024-10-05 06:43:15,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:43:15,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:43:15,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:43:15,039 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:43:15,052 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Working directory for job is: /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs.runners DEBUG 2024-10-05 06:43:15,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [77] queued (32.752 ms) +galaxy.jobs.handler INFO 2024-10-05 06:43:15,062 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 77 +tpv.core.entities DEBUG 2024-10-05 06:43:15,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:43:15,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:43:15,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:43:15,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:43:15,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Working directory for job is: /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs.runners DEBUG 2024-10-05 06:43:15,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [78] queued (50.039 ms) +galaxy.jobs.handler INFO 2024-10-05 06:43:15,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 78 +tpv.core.entities DEBUG 2024-10-05 06:43:15,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:43:15,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:43:15,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:43:15,171 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:43:15,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [77] prepared (113.376 ms) +galaxy.jobs DEBUG 2024-10-05 06:43:15,206 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Working directory for job is: /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs.runners DEBUG 2024-10-05 06:43:15,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [79] queued (59.414 ms) +galaxy.jobs.handler INFO 2024-10-05 06:43:15,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.command_factory INFO 2024-10-05 06:43:15,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/77/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/77/registry.xml' '/galaxy/server/database/jobs_directory/000/77/upload_params.json' '105:/galaxy/server/database/objects/8/7/a/dataset_87ad91d1-3029-4d89-b0a0-901ce3fee026_files:/galaxy/server/database/objects/8/7/a/dataset_87ad91d1-3029-4d89-b0a0-901ce3fee026.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 79 +galaxy.jobs.runners DEBUG 2024-10-05 06:43:15,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (77) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/77/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/77/galaxy_77.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:43:15,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [78] prepared (100.868 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:43:15,286 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/78/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/78/registry.xml' '/galaxy/server/database/jobs_directory/000/78/upload_params.json' '106:/galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02_files:/galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:43:15,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (78) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/78/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/78/galaxy_78.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 78 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:43:15,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [79] prepared (93.147 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 78 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:43:15,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/79/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/79/registry.xml' '/galaxy/server/database/jobs_directory/000/79/upload_params.json' '107:/galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac_files:/galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:43:15,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (79) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/79/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/79/galaxy_79.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 79 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 79 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:15,984 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:16,033 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:26,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xh74b with k8s id: gxy-xh74b succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:43:26,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 77: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:27,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7rlv4 with k8s id: gxy-7rlv4 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:27,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4hwxw with k8s id: gxy-4hwxw succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:43:27,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 78: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:43:27,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:43:40,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 77 finished +galaxy.model.metadata DEBUG 2024-10-05 06:43:40,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 105 +galaxy.jobs INFO 2024-10-05 06:43:40,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 77 in /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs DEBUG 2024-10-05 06:43:40,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 77 executed (221.594 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:40,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:43:41,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2024-10-05 06:43:41,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 107 +galaxy.jobs.runners DEBUG 2024-10-05 06:43:41,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 78 finished +galaxy.jobs INFO 2024-10-05 06:43:41,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.model.metadata DEBUG 2024-10-05 06:43:41,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 106 +galaxy.jobs INFO 2024-10-05 06:43:41,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs DEBUG 2024-10-05 06:43:41,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 79 executed (114.904 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:41,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 79 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:43:41,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 78 executed (103.201 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:41,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 78 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:43:43,022 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 80 +tpv.core.entities DEBUG 2024-10-05 06:43:43,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/.*, abstract=False, cores=8, mem=20, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:43:43,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:43:43,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:43:43,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:43:43,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Working directory for job is: /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs.runners DEBUG 2024-10-05 06:43:43,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [80] queued (39.347 ms) +galaxy.jobs.handler INFO 2024-10-05 06:43:43,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:43,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 80 +galaxy.jobs DEBUG 2024-10-05 06:43:43,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [80] prepared (65.315 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:43:43,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:43:43,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:43:43,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:43:43,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/8/7/a/dataset_87ad91d1-3029-4d89-b0a0-901ce3fee026.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" 'localref.fa' '/galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat' > second.sai && bwa sampe -r '@RG\tID:rg1\tPL:CAPILLARY' 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat' '/galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/galaxy/server/database/objects/7/c/d/dataset_7cd11f28-de6c-4ce2-a83c-2a96abd481cc.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:43:43,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (80) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/80/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/80/galaxy_80.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:43,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 80 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:43:43,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:43:43,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18: mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e +galaxy.tool_util.deps.containers INFO 2024-10-05 06:43:43,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:43,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 80 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:43,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:47,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ql45j with k8s id: gxy-ql45j succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:43:47,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 80: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:43:56,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 80 finished +galaxy.model.metadata DEBUG 2024-10-05 06:43:56,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2024-10-05 06:43:56,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 80 in /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs DEBUG 2024-10-05 06:43:56,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 80 executed (99.761 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:43:56,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 80 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:44:00,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 81 +tpv.core.entities DEBUG 2024-10-05 06:44:00,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:44:00,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:44:00,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:44:00,515 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:44:00,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Working directory for job is: /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs.runners DEBUG 2024-10-05 06:44:00,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [81] queued (35.382 ms) +galaxy.jobs.handler INFO 2024-10-05 06:44:00,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:00,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 81 +galaxy.jobs DEBUG 2024-10-05 06:44:00,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [81] prepared (83.105 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:44:00,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/81/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/81/registry.xml' '/galaxy/server/database/jobs_directory/000/81/upload_params.json' '109:/galaxy/server/database/objects/4/9/5/dataset_49531fc3-a85c-4d5c-bef9-2e148d0f4acd_files:/galaxy/server/database/objects/4/9/5/dataset_49531fc3-a85c-4d5c-bef9-2e148d0f4acd.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:44:00,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (81) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/81/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/81/galaxy_81.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:00,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 81 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:00,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 81 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:01,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:12,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rns6p with k8s id: gxy-rns6p succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:44:12,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 81: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:44:22,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 81 finished +galaxy.model.metadata DEBUG 2024-10-05 06:44:22,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2024-10-05 06:44:22,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs DEBUG 2024-10-05 06:44:22,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 81 executed (93.151 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:22,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 81 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:44:22,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82 +tpv.core.entities DEBUG 2024-10-05 06:44:23,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/.*, abstract=False, cores=1, mem=11.4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:44:23,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:44:23,007 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:44:23,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:44:23,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Working directory for job is: /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs.runners DEBUG 2024-10-05 06:44:23,039 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [82] queued (32.161 ms) +galaxy.jobs.handler INFO 2024-10-05 06:44:23,042 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:23,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 82 +galaxy.jobs DEBUG 2024-10-05 06:44:23,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [82] prepared (44.536 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:44:23,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:44:23,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:44:23,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:44:23,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/82/tool_script.sh] for tool command [poretools qualdist '/galaxy/server/database/objects/4/9/5/dataset_49531fc3-a85c-4d5c-bef9-2e148d0f4acd.dat' > '/galaxy/server/database/objects/1/a/8/dataset_1a8f3133-7610-4b69-892f-bd8efca3e72d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:44:23,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (82) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/82/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/82/galaxy_82.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:23,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 82 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:44:23,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:44:23,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:44:23,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:23,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 82 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:23,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:44:53,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5qlk7 with k8s id: gxy-5qlk7 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:44:53,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 82: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:45:02,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 82 finished +galaxy.model.metadata DEBUG 2024-10-05 06:45:02,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 110 +galaxy.jobs INFO 2024-10-05 06:45:02,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs DEBUG 2024-10-05 06:45:02,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 82 executed (94.367 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:02,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 82 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:45:04,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2024-10-05 06:45:04,894 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:45:04,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:45:04,899 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:45:04,911 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:45:04,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Working directory for job is: /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs.runners DEBUG 2024-10-05 06:45:04,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [83] queued (34.823 ms) +galaxy.jobs.handler INFO 2024-10-05 06:45:04,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:04,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 83 +galaxy.jobs DEBUG 2024-10-05 06:45:05,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [83] prepared (75.973 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:45:05,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/83/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/83/registry.xml' '/galaxy/server/database/jobs_directory/000/83/upload_params.json' '111:/galaxy/server/database/objects/a/7/4/dataset_a74e2bbb-94df-4176-bcac-cda666391a8a_files:/galaxy/server/database/objects/a/7/4/dataset_a74e2bbb-94df-4176-bcac-cda666391a8a.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:45:05,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (83) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/83/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/83/galaxy_83.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:05,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 83 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:05,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 83 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:05,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:16,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-nxr9b with k8s id: gxy-nxr9b succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:45:16,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:45:26,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2024-10-05 06:45:26,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 111 +galaxy.jobs INFO 2024-10-05 06:45:26,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2024-10-05 06:45:26,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 83 executed (86.067 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:26,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 83 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:45:27,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84 +tpv.core.entities DEBUG 2024-10-05 06:45:27,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/.*, abstract=False, cores=1, mem=11.4, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:45:27,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:45:27,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:45:27,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:45:27,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Working directory for job is: /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs.runners DEBUG 2024-10-05 06:45:27,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [84] queued (33.238 ms) +galaxy.jobs.handler INFO 2024-10-05 06:45:27,473 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:27,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 84 +galaxy.jobs DEBUG 2024-10-05 06:45:27,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [84] prepared (41.304 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:27,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:45:27,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:27,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:45:27,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/84/tool_script.sh] for tool command [poretools qualdist '/galaxy/server/database/objects/a/7/4/dataset_a74e2bbb-94df-4176-bcac-cda666391a8a.dat' > '/galaxy/server/database/objects/6/b/b/dataset_6bb58ad4-0dd4-44b1-a170-0b2e6aac5738.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:45:27,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (84) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/84/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/84/galaxy_84.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:27,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:27,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:45:27,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:27,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:27,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:28,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zmnpq failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-zmnpq. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:45:32,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-zmnpq + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-zmnpq": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (84/gxy-zmnpq) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (84/gxy-zmnpq) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (84/gxy-zmnpq) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (84/gxy-zmnpq) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-zmnpq. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Attempting to stop job 84 (gxy-zmnpq) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Found job with id gxy-zmnpq to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:32,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (84/gxy-zmnpq) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-10-05 06:45:35,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 86, 85 +tpv.core.entities DEBUG 2024-10-05 06:45:35,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:45:35,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:45:35,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:45:35,666 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:45:35,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Working directory for job is: /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs.runners DEBUG 2024-10-05 06:45:35,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [85] queued (32.007 ms) +galaxy.jobs.handler INFO 2024-10-05 06:45:35,689 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:35,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 85 +tpv.core.entities DEBUG 2024-10-05 06:45:35,703 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:45:35,703 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:45:35,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:45:35,721 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:45:35,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Working directory for job is: /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs.runners DEBUG 2024-10-05 06:45:35,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [86] queued (45.363 ms) +galaxy.jobs.handler INFO 2024-10-05 06:45:35,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:35,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 86 +galaxy.jobs DEBUG 2024-10-05 06:45:35,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [85] prepared (102.823 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:45:35,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/85/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/85/registry.xml' '/galaxy/server/database/jobs_directory/000/85/upload_params.json' '113:/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d_files:/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:45:35,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (85) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/85/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/85/galaxy_85.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:45:35,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [86] prepared (80.046 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:35,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 85 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:35,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 85 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:45:35,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/86/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/86/registry.xml' '/galaxy/server/database/jobs_directory/000/86/upload_params.json' '114:/galaxy/server/database/objects/4/d/5/dataset_4d569c1c-180f-4101-9377-2c89a23af474_files:/galaxy/server/database/objects/4/d/5/dataset_4d569c1c-180f-4101-9377-2c89a23af474.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:45:35,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (86) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/86/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/86/galaxy_86.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:35,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 86 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:35,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 86 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:36,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:36,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:47,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-szdgr with k8s id: gxy-szdgr succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:47,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j72jb with k8s id: gxy-j72jb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:45:47,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 85: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:45:47,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 86: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:45:56,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 85 finished +galaxy.model.metadata DEBUG 2024-10-05 06:45:56,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 113 +galaxy.jobs INFO 2024-10-05 06:45:56,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 85 in /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs DEBUG 2024-10-05 06:45:56,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 85 executed (107.734 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:56,959 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 85 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:45:57,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2024-10-05 06:45:57,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 114 +galaxy.jobs INFO 2024-10-05 06:45:57,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2024-10-05 06:45:57,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 86 executed (90.997 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:57,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 86 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:45:58,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 87 +tpv.core.entities DEBUG 2024-10-05 06:45:58,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:45:58,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:45:58,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:45:58,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:45:58,292 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Working directory for job is: /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs.runners DEBUG 2024-10-05 06:45:58,301 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [87] queued (40.814 ms) +galaxy.jobs.handler INFO 2024-10-05 06:45:58,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:58,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 87 +galaxy.jobs DEBUG 2024-10-05 06:45:58,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [87] prepared (74.256 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:58,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:45:58,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:58,594 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:45:58,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/87/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/87/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/4/d/5/dataset_4d569c1c-180f-4101-9377-2c89a23af474.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > expression_matrix.txt && cut -f 6 body.txt > gene_lengths.txt && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak && mv -f expression_matrix.txt.bak '/galaxy/server/database/objects/c/1/5/dataset_c15fc5f4-ca6d-46a9-a281-eba651b0adc2.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/f/4/1/dataset_f41fef77-9444-46f7-9667-d291348a7939.dat' && sed -e 's|/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/4/a/e/dataset_4ae0839d-f4e4-4911-95fc-93de9f59667c.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:45:58,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (87) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/87/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/87/galaxy_87.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:58,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 87 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:58,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:45:58,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:45:58,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:58,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 87 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:45:59,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:07,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pfkx9 with k8s id: gxy-pfkx9 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:46:07,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 87: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:46:16,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 87 finished +galaxy.model.metadata DEBUG 2024-10-05 06:46:16,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 115 +galaxy.model.metadata DEBUG 2024-10-05 06:46:16,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 116 +galaxy.model.metadata DEBUG 2024-10-05 06:46:16,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 117 +galaxy.util WARNING 2024-10-05 06:46:16,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/1/5/dataset_c15fc5f4-ca6d-46a9-a281-eba651b0adc2.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/1/5/dataset_c15fc5f4-ca6d-46a9-a281-eba651b0adc2.dat' +galaxy.jobs INFO 2024-10-05 06:46:16,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 87 in /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs DEBUG 2024-10-05 06:46:16,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 87 executed (131.648 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:16,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 87 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:46:18,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 89, 88 +tpv.core.entities DEBUG 2024-10-05 06:46:18,794 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:46:18,795 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:46:18,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:46:18,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:46:18,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Working directory for job is: /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-10-05 06:46:18,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [88] queued (33.462 ms) +galaxy.jobs.handler INFO 2024-10-05 06:46:18,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:18,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 88 +tpv.core.entities DEBUG 2024-10-05 06:46:18,848 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:46:18,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:46:18,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:46:18,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:46:18,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Working directory for job is: /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs.runners DEBUG 2024-10-05 06:46:18,903 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [89] queued (49.624 ms) +galaxy.jobs.handler INFO 2024-10-05 06:46:18,905 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:18,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 89 +galaxy.jobs DEBUG 2024-10-05 06:46:18,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [88] prepared (90.516 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:46:18,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/88/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/88/registry.xml' '/galaxy/server/database/jobs_directory/000/88/upload_params.json' '118:/galaxy/server/database/objects/d/6/c/dataset_d6cc9a3c-d14e-4b20-94b6-482853ff7fcb_files:/galaxy/server/database/objects/d/6/c/dataset_d6cc9a3c-d14e-4b20-94b6-482853ff7fcb.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:46:18,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (88) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/88/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/88/galaxy_88.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:46:18,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [89] prepared (80.389 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:19,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 88 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:46:19,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/89/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/89/registry.xml' '/galaxy/server/database/jobs_directory/000/89/upload_params.json' '119:/galaxy/server/database/objects/0/b/a/dataset_0baaabba-42cc-4a33-b831-6cf2d8c991c7_files:/galaxy/server/database/objects/0/b/a/dataset_0baaabba-42cc-4a33-b831-6cf2d8c991c7.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:46:19,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (89) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/89/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/89/galaxy_89.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:19,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 88 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:19,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 89 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:19,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 89 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:20,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:20,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cd72l failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-cd72l. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 89 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (89/gxy-cd72l) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (89/gxy-cd72l) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (89/gxy-cd72l) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (89/gxy-cd72l) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-cd72l. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Attempting to stop job 89 (gxy-cd72l) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Could not find job with id gxy-cd72l to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:29,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (89/gxy-cd72l) Terminated at user's request +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:30,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-6nxf6 with k8s id: gxy-6nxf6 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:46:30,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 88: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:46:40,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2024-10-05 06:46:40,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 118 +galaxy.jobs INFO 2024-10-05 06:46:40,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 88 in /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs DEBUG 2024-10-05 06:46:40,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 88 executed (115.935 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:40,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 88 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:46:41,533 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90, 91 +tpv.core.entities DEBUG 2024-10-05 06:46:41,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:46:41,563 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:46:41,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:46:41,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:46:41,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Working directory for job is: /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs.runners DEBUG 2024-10-05 06:46:41,600 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [90] queued (32.782 ms) +galaxy.jobs.handler INFO 2024-10-05 06:46:41,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 90 +tpv.core.entities DEBUG 2024-10-05 06:46:41,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:46:41,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:46:41,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:46:41,632 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:46:41,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Working directory for job is: /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs.runners DEBUG 2024-10-05 06:46:41,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [91] queued (53.564 ms) +galaxy.jobs.handler INFO 2024-10-05 06:46:41,676 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 91 +galaxy.jobs DEBUG 2024-10-05 06:46:41,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [90] prepared (105.445 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:46:41,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/90/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/90/registry.xml' '/galaxy/server/database/jobs_directory/000/90/upload_params.json' '120:/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6_files:/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:46:41,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (90) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/90/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/90/galaxy_90.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:46:41,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [91] prepared (80.930 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 90 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 90 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:46:41,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/91/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/91/registry.xml' '/galaxy/server/database/jobs_directory/000/91/upload_params.json' '121:/galaxy/server/database/objects/c/0/0/dataset_c00c209c-ba23-4de9-be4f-b3131f056a32_files:/galaxy/server/database/objects/c/0/0/dataset_c00c209c-ba23-4de9-be4f-b3131f056a32.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:46:41,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (91) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/91/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/91/galaxy_91.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 91 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 91 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:41,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:42,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:53,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xv286 with k8s id: gxy-xv286 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:46:53,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hb8qv with k8s id: gxy-hb8qv succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:46:53,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 90: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:46:53,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:47:03,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2024-10-05 06:47:03,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 121 +galaxy.jobs.runners DEBUG 2024-10-05 06:47:03,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 90 finished +galaxy.jobs INFO 2024-10-05 06:47:03,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 91 in /galaxy/server/database/jobs_directory/000/91 +galaxy.model.metadata DEBUG 2024-10-05 06:47:03,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 120 +galaxy.jobs INFO 2024-10-05 06:47:03,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 90 in /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs DEBUG 2024-10-05 06:47:03,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 91 executed (135.897 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:03,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 91 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:47:03,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 90 executed (116.348 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:03,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 90 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:47:04,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 92 +tpv.core.entities DEBUG 2024-10-05 06:47:04,179 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:47:04,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:47:04,184 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:47:04,196 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:47:04,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Working directory for job is: /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs.runners DEBUG 2024-10-05 06:47:04,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [92] queued (38.264 ms) +galaxy.jobs.handler INFO 2024-10-05 06:47:04,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:04,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 92 +galaxy.jobs DEBUG 2024-10-05 06:47:04,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [92] prepared (58.347 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:47:04,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:47:04,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:47:04,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:47:04,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/92/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/92/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/c/0/0/dataset_c00c209c-ba23-4de9-be4f-b3131f056a32.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' -J --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/0/b/e/dataset_0be0c78c-5e01-4d18-adec-2a8f203d15b2.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/d/8/1/dataset_d8140b51-b41f-4eb2-b71b-2aec404a5274.dat' && sed -e 's|/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat|featureCounts_input1.bam|g' 'output.jcounts' > '/galaxy/server/database/objects/9/f/9/dataset_9f90f531-a99b-4748-b642-68cadf49fcc0.dat' && sed -e 's|/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/c/9/6/dataset_c9604cc7-11a5-4d42-b278-aad5a8b229cf.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:47:04,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (92) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/92/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/92/galaxy_92.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:04,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 92 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:47:04,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:47:04,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:47:04,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:04,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 92 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:05,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:09,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-69c67 with k8s id: gxy-69c67 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:47:09,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 92: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:47:18,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 92 finished +galaxy.model.metadata DEBUG 2024-10-05 06:47:18,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 122 +galaxy.model.metadata DEBUG 2024-10-05 06:47:18,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 123 +galaxy.model.metadata DEBUG 2024-10-05 06:47:18,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 124 +galaxy.model.metadata DEBUG 2024-10-05 06:47:18,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 125 +galaxy.jobs INFO 2024-10-05 06:47:19,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs DEBUG 2024-10-05 06:47:19,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 92 executed (144.850 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:19,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 92 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:47:21,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 93 +tpv.core.entities DEBUG 2024-10-05 06:47:21,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:47:21,622 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:47:21,625 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:47:21,636 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:47:21,649 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Working directory for job is: /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs.runners DEBUG 2024-10-05 06:47:21,656 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [93] queued (30.387 ms) +galaxy.jobs.handler INFO 2024-10-05 06:47:21,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:21,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 93 +galaxy.jobs DEBUG 2024-10-05 06:47:21,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [93] prepared (76.120 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:47:21,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/93/registry.xml' '/galaxy/server/database/jobs_directory/000/93/upload_params.json' '126:/galaxy/server/database/objects/a/a/7/dataset_aa7e61ab-ea33-46bc-be7a-d855d34b84cc_files:/galaxy/server/database/objects/a/a/7/dataset_aa7e61ab-ea33-46bc-be7a-d855d34b84cc.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:47:21,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (93) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/93/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/93/galaxy_93.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:21,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 93 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:21,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 93 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:22,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:33,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wj9z8 with k8s id: gxy-wj9z8 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:47:33,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 93: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:47:42,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 93 finished +galaxy.model.metadata DEBUG 2024-10-05 06:47:43,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 126 +galaxy.jobs INFO 2024-10-05 06:47:43,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs DEBUG 2024-10-05 06:47:43,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 93 executed (115.902 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:43,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 93 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:47:44,091 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94 +tpv.core.entities DEBUG 2024-10-05 06:47:44,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:47:44,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:47:44,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:47:44,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:47:44,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Working directory for job is: /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs.runners DEBUG 2024-10-05 06:47:44,159 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [94] queued (34.556 ms) +galaxy.jobs.handler INFO 2024-10-05 06:47:44,161 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:44,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 94 +galaxy.jobs DEBUG 2024-10-05 06:47:44,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [94] prepared (83.692 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:47:44,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/94/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/94/registry.xml' '/galaxy/server/database/jobs_directory/000/94/upload_params.json' '127:/galaxy/server/database/objects/d/d/8/dataset_dd8f2886-0f61-4638-83b0-b73e49bf6c68_files:/galaxy/server/database/objects/d/d/8/dataset_dd8f2886-0f61-4638-83b0-b73e49bf6c68.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:47:44,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (94) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/94/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/94/galaxy_94.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:44,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 94 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:44,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 94 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:44,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:47:54,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cz5g7 with k8s id: gxy-cz5g7 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:47:55,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 94: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:48:04,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 94 finished +galaxy.model.metadata DEBUG 2024-10-05 06:48:04,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 127 +galaxy.jobs INFO 2024-10-05 06:48:04,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs DEBUG 2024-10-05 06:48:04,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 94 executed (103.342 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:04,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 94 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:48:05,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 95 +tpv.core.entities DEBUG 2024-10-05 06:48:05,593 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:48:05,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:48:05,598 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:48:05,610 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:48:05,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Working directory for job is: /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs.runners DEBUG 2024-10-05 06:48:05,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [95] queued (32.265 ms) +galaxy.jobs.handler INFO 2024-10-05 06:48:05,632 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:05,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 95 +galaxy.jobs DEBUG 2024-10-05 06:48:05,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [95] prepared (79.326 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:48:05,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/95/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/95/registry.xml' '/galaxy/server/database/jobs_directory/000/95/upload_params.json' '128:/galaxy/server/database/objects/3/a/3/dataset_3a3b7620-7a56-4671-91fa-d31c73ede79a_files:/galaxy/server/database/objects/3/a/3/dataset_3a3b7620-7a56-4671-91fa-d31c73ede79a.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:48:05,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (95) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/95/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/95/galaxy_95.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:05,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 95 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:05,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 95 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:06,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:17,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-f94vn with k8s id: gxy-f94vn succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:48:17,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 95: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:48:26,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 95 finished +galaxy.model.metadata DEBUG 2024-10-05 06:48:26,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 128 +galaxy.jobs INFO 2024-10-05 06:48:26,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 95 in /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs DEBUG 2024-10-05 06:48:26,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 95 executed (95.166 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:26,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 95 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:48:28,053 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 97, 96 +tpv.core.entities DEBUG 2024-10-05 06:48:28,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:48:28,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:48:28,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:48:28,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:48:28,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Working directory for job is: /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs.runners DEBUG 2024-10-05 06:48:28,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [96] queued (35.811 ms) +galaxy.jobs.handler INFO 2024-10-05 06:48:28,127 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:28,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 96 +tpv.core.entities DEBUG 2024-10-05 06:48:28,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:48:28,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:48:28,144 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:48:28,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:48:28,184 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Working directory for job is: /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs.runners DEBUG 2024-10-05 06:48:28,192 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [97] queued (47.547 ms) +galaxy.jobs.handler INFO 2024-10-05 06:48:28,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:28,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 97 +galaxy.jobs DEBUG 2024-10-05 06:48:28,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [96] prepared (102.899 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:48:28,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/96/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '129:/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964_files:/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:48:28,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (96) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/96/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/96/galaxy_96.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:48:28,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [97] prepared (83.625 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:28,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 96 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:28,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 96 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:48:28,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/97/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/97/registry.xml' '/galaxy/server/database/jobs_directory/000/97/upload_params.json' '130:/galaxy/server/database/objects/5/0/d/dataset_50de0387-e47c-431d-b148-bcedfa1b1742_files:/galaxy/server/database/objects/5/0/d/dataset_50de0387-e47c-431d-b148-bcedfa1b1742.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:48:28,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (97) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/97/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/97/galaxy_97.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:28,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 97 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:28,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 97 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:29,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:29,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:39,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tmcw8 with k8s id: gxy-tmcw8 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:48:39,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 97: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:40,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-t5pg9 with k8s id: gxy-t5pg9 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:48:40,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 96: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:48:49,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 97 finished +galaxy.model.metadata DEBUG 2024-10-05 06:48:49,526 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 130 +galaxy.jobs INFO 2024-10-05 06:48:49,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 97 in /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs DEBUG 2024-10-05 06:48:49,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 97 executed (103.576 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:49,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 97 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:48:50,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 96 finished +galaxy.model.metadata DEBUG 2024-10-05 06:48:50,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 129 +galaxy.jobs INFO 2024-10-05 06:48:50,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 96 in /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs DEBUG 2024-10-05 06:48:50,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 96 executed (145.267 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:50,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 96 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:48:50,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 98 +tpv.core.entities DEBUG 2024-10-05 06:48:50,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:48:50,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:48:50,719 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:48:50,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:48:50,751 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Working directory for job is: /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs.runners DEBUG 2024-10-05 06:48:50,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [98] queued (42.061 ms) +galaxy.jobs.handler INFO 2024-10-05 06:48:50,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:50,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 98 +galaxy.jobs DEBUG 2024-10-05 06:48:50,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [98] prepared (64.545 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:48:50,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:48:50,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:48:51,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:48:51,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/98/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/98/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/5/0/d/dataset_50de0387-e47c-431d-b148-bcedfa1b1742.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 -R BAM '/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat|subset.sorted.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/3/7/e/dataset_37e3acb7-6871-418f-9c0f-cb8da855a047.dat' && samtools sort --no-PG -o '/galaxy/server/database/objects/2/9/5/dataset_295c8a84-b75c-43d0-a668-eeb0c4fcdc75.dat' -@ ${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" *.featureCounts.bam && sed -e 's|/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat|subset.sorted.bam|g' 'output.summary' > '/galaxy/server/database/objects/0/d/a/dataset_0da052b4-da72-49ac-9db0-f10b591f53b5.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:48:51,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (98) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/98/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/98/galaxy_98.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:51,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 98 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:48:51,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:48:51,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:48:51,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:51,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 98 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:51,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:48:55,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-l8lcb with k8s id: gxy-l8lcb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:48:55,799 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 98: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:49:04,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 98 finished +galaxy.model.metadata DEBUG 2024-10-05 06:49:05,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 131 +galaxy.model.metadata DEBUG 2024-10-05 06:49:05,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 132 +galaxy.model.metadata DEBUG 2024-10-05 06:49:05,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 133 +galaxy.jobs INFO 2024-10-05 06:49:05,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 98 in /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs DEBUG 2024-10-05 06:49:05,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 98 executed (170.646 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:05,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 98 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:49:08,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 99 +tpv.core.entities DEBUG 2024-10-05 06:49:08,127 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:49:08,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:49:08,131 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:49:08,144 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:49:08,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Working directory for job is: /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs.runners DEBUG 2024-10-05 06:49:08,165 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [99] queued (33.571 ms) +galaxy.jobs.handler INFO 2024-10-05 06:49:08,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:08,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 99 +galaxy.jobs DEBUG 2024-10-05 06:49:08,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [99] prepared (76.012 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:49:08,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/99/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/99/registry.xml' '/galaxy/server/database/jobs_directory/000/99/upload_params.json' '134:/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae_files:/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:49:08,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (99) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/99/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/99/galaxy_99.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:08,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 99 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:08,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 99 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:08,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:49:09,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 100 +tpv.core.entities DEBUG 2024-10-05 06:49:09,198 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:49:09,198 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:49:09,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:49:09,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:49:09,226 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Working directory for job is: /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs.runners DEBUG 2024-10-05 06:49:09,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [100] queued (31.478 ms) +galaxy.jobs.handler INFO 2024-10-05 06:49:09,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:09,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 100 +galaxy.jobs DEBUG 2024-10-05 06:49:09,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [100] prepared (71.820 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:49:09,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/100/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/100/registry.xml' '/galaxy/server/database/jobs_directory/000/100/upload_params.json' '135:/galaxy/server/database/objects/c/e/7/dataset_ce77ae28-4aca-40ef-a60e-83006ca51482_files:/galaxy/server/database/objects/c/e/7/dataset_ce77ae28-4aca-40ef-a60e-83006ca51482.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:49:09,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (100) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/100/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/100/galaxy_100.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:09,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 100 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:09,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 100 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:09,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:19,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rnfmr with k8s id: gxy-rnfmr succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:49:20,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 99: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:21,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8ns8r with k8s id: gxy-8ns8r succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:49:21,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 100: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:49:29,589 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 99 finished +galaxy.model.metadata DEBUG 2024-10-05 06:49:29,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 134 +galaxy.jobs INFO 2024-10-05 06:49:29,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 99 in /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs DEBUG 2024-10-05 06:49:29,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 99 executed (104.087 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:29,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 99 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:49:30,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 100 finished +galaxy.model.metadata DEBUG 2024-10-05 06:49:30,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 135 +galaxy.jobs INFO 2024-10-05 06:49:30,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 100 in /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs DEBUG 2024-10-05 06:49:30,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 100 executed (147.294 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:30,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 100 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:49:30,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 101 +tpv.core.entities DEBUG 2024-10-05 06:49:30,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:49:30,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:49:30,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:49:30,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:49:30,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Working directory for job is: /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs.runners DEBUG 2024-10-05 06:49:30,893 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [101] queued (37.988 ms) +galaxy.jobs.handler INFO 2024-10-05 06:49:30,896 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:30,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 101 +galaxy.jobs DEBUG 2024-10-05 06:49:30,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [101] prepared (65.860 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:49:30,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:49:30,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:49:30,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:49:31,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/101/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/101/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/c/e/7/dataset_ce77ae28-4aca-40ef-a60e-83006ca51482.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > expression_matrix.txt && cut -f 6 body.txt > gene_lengths.txt && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak && mv -f expression_matrix.txt.bak '/galaxy/server/database/objects/5/e/4/dataset_5e46e6cb-0335-4e28-8bd8-5bb6c091bc9b.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/6/0/4/dataset_60420d9e-7c27-4816-8e21-c1f28a7c9693.dat' && sed -e 's|/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/c/a/2/dataset_ca2c6ea1-7497-453a-8536-06373b8549d4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:49:31,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (101) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/101/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/101/galaxy_101.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:31,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 101 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:49:31,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:49:31,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:49:31,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:31,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 101 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:32,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:36,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tb28m with k8s id: gxy-tb28m succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:49:36,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 101: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:49:45,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 101 finished +galaxy.model.metadata DEBUG 2024-10-05 06:49:45,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 136 +galaxy.model.metadata DEBUG 2024-10-05 06:49:45,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 137 +galaxy.model.metadata DEBUG 2024-10-05 06:49:45,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 138 +galaxy.util WARNING 2024-10-05 06:49:45,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/e/4/dataset_5e46e6cb-0335-4e28-8bd8-5bb6c091bc9b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/e/4/dataset_5e46e6cb-0335-4e28-8bd8-5bb6c091bc9b.dat' +galaxy.jobs INFO 2024-10-05 06:49:45,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 101 in /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs DEBUG 2024-10-05 06:49:45,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 101 executed (122.657 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:45,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 101 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:49:47,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 102 +tpv.core.entities DEBUG 2024-10-05 06:49:47,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:49:47,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:49:47,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:49:47,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:49:47,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Working directory for job is: /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs.runners DEBUG 2024-10-05 06:49:47,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [102] queued (30.664 ms) +galaxy.jobs.handler INFO 2024-10-05 06:49:47,279 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:47,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 102 +galaxy.jobs DEBUG 2024-10-05 06:49:47,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [102] prepared (75.905 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:49:47,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/102/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/102/registry.xml' '/galaxy/server/database/jobs_directory/000/102/upload_params.json' '139:/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567_files:/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:49:47,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (102) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/102/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/102/galaxy_102.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:47,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 102 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:47,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 102 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:48,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:49:48,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 103 +tpv.core.entities DEBUG 2024-10-05 06:49:48,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:49:48,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:49:48,320 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:49:48,333 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:49:48,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Working directory for job is: /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs.runners DEBUG 2024-10-05 06:49:48,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [103] queued (34.644 ms) +galaxy.jobs.handler INFO 2024-10-05 06:49:48,358 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:48,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 103 +galaxy.jobs DEBUG 2024-10-05 06:49:48,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [103] prepared (77.660 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:49:48,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/103/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/103/registry.xml' '/galaxy/server/database/jobs_directory/000/103/upload_params.json' '140:/galaxy/server/database/objects/d/6/8/dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf_files:/galaxy/server/database/objects/d/6/8/dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:49:48,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (103) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/103/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/103/galaxy_103.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:48,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 103 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:48,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 103 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:49,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:58,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5xwpz with k8s id: gxy-5xwpz succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:49:58,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 102: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:49:59,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cmlt6 with k8s id: gxy-cmlt6 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:49:59,589 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 103: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:50:08,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 102 finished +galaxy.model.metadata DEBUG 2024-10-05 06:50:08,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 139 +galaxy.jobs INFO 2024-10-05 06:50:08,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 102 in /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs DEBUG 2024-10-05 06:50:08,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 102 executed (105.156 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:08,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 102 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:50:09,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 103 finished +galaxy.model.metadata DEBUG 2024-10-05 06:50:09,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 140 +galaxy.jobs INFO 2024-10-05 06:50:09,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 103 in /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs DEBUG 2024-10-05 06:50:09,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 103 executed (89.751 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:09,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 103 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:50:09,861 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 104 +tpv.core.entities DEBUG 2024-10-05 06:50:09,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:50:09,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:50:09,899 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:50:09,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:50:09,932 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Working directory for job is: /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs.runners DEBUG 2024-10-05 06:50:09,942 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [104] queued (42.326 ms) +galaxy.jobs.handler INFO 2024-10-05 06:50:09,944 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:09,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 104 +galaxy.jobs DEBUG 2024-10-05 06:50:10,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [104] prepared (72.847 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:10,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:50:10,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:10,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:50:10,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/104/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/104/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/d/6/8/dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat|featureCounts_input1.bam|g' > body.txt && cp body.txt '/galaxy/server/database/objects/5/5/5/dataset_555e8a75-cf5f-4ab4-a2c2-9fd96f79b13a.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/3/4/9/dataset_349325ea-bd0d-4387-8723-817a14ab3c2c.dat' && sed -e 's|/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/4/2/0/dataset_420d6bb8-9b15-4da7-8aba-54e0a92dd8b9.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:50:10,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (104) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/104/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/104/galaxy_104.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:10,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 104 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:10,112 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:50:10,112 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:10,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:10,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 104 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:10,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:15,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4bm9g with k8s id: gxy-4bm9g succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:50:15,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 104: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:50:25,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 104 finished +galaxy.model.metadata DEBUG 2024-10-05 06:50:25,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 141 +galaxy.model.metadata DEBUG 2024-10-05 06:50:25,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 142 +galaxy.model.metadata DEBUG 2024-10-05 06:50:25,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 143 +galaxy.util WARNING 2024-10-05 06:50:25,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/5/5/dataset_555e8a75-cf5f-4ab4-a2c2-9fd96f79b13a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/5/5/dataset_555e8a75-cf5f-4ab4-a2c2-9fd96f79b13a.dat' +galaxy.jobs INFO 2024-10-05 06:50:25,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 104 in /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs DEBUG 2024-10-05 06:50:25,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 104 executed (145.329 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:25,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 104 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:50:27,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 106, 105 +tpv.core.entities DEBUG 2024-10-05 06:50:27,392 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:50:27,393 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:50:27,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:50:27,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:50:27,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Working directory for job is: /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs.runners DEBUG 2024-10-05 06:50:27,434 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [105] queued (36.459 ms) +galaxy.jobs.handler INFO 2024-10-05 06:50:27,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 105 +tpv.core.entities DEBUG 2024-10-05 06:50:27,448 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:50:27,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:50:27,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:50:27,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:50:27,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Working directory for job is: /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs.runners DEBUG 2024-10-05 06:50:27,500 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [106] queued (46.304 ms) +galaxy.jobs.handler INFO 2024-10-05 06:50:27,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 106 +galaxy.jobs DEBUG 2024-10-05 06:50:27,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [105] prepared (102.292 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:50:27,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/105/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/105/registry.xml' '/galaxy/server/database/jobs_directory/000/105/upload_params.json' '144:/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1_files:/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:50:27,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (105) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/105/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/105/galaxy_105.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:50:27,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [106] prepared (82.837 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 105 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 105 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:50:27,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/106/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/106/registry.xml' '/galaxy/server/database/jobs_directory/000/106/upload_params.json' '145:/galaxy/server/database/objects/4/b/d/dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2_files:/galaxy/server/database/objects/4/b/d/dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:50:27,630 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (106) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/106/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/106/galaxy_106.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 106 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 106 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:27,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:28,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:39,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-bpkq8 with k8s id: gxy-bpkq8 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:39,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-q7xtt with k8s id: gxy-q7xtt succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:50:39,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 105: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:50:39,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 106: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:50:48,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 105 finished +galaxy.model.metadata DEBUG 2024-10-05 06:50:48,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 144 +galaxy.jobs INFO 2024-10-05 06:50:48,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 105 in /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs.runners DEBUG 2024-10-05 06:50:48,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 106 finished +galaxy.jobs DEBUG 2024-10-05 06:50:49,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 105 executed (104.802 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:49,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 105 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-10-05 06:50:49,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 145 +galaxy.jobs INFO 2024-10-05 06:50:49,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 106 in /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs DEBUG 2024-10-05 06:50:49,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 106 executed (122.528 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:49,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 106 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:50:50,134 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 107 +tpv.core.entities DEBUG 2024-10-05 06:50:50,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:50:50,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:50:50,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:50:50,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:50:50,208 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Working directory for job is: /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs.runners DEBUG 2024-10-05 06:50:50,219 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [107] queued (46.107 ms) +galaxy.jobs.handler INFO 2024-10-05 06:50:50,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:50,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 107 +galaxy.jobs DEBUG 2024-10-05 06:50:50,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [107] prepared (73.771 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:50,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:50:50,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:50,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:50:50,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/107/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/107/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/4/b/d/dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' -J --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/2/1/c/dataset_21c1b12d-0965-479d-8dcc-ce8b567bc557.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/e/2/7/dataset_e277f8ed-1eb5-44e3-a4f8-5c88b87b9f4b.dat' && sed -e 's|/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat|featureCounts_input1.bam|g' 'output.jcounts' > '/galaxy/server/database/objects/5/8/a/dataset_58ae8aaf-435f-4432-b313-0f307bfb219e.dat' && sed -e 's|/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/b/5/1/dataset_b511b760-4917-4d63-bf70-ed5c6fdcab2b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:50:50,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (107) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/107/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/107/galaxy_107.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:50,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:50,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:50:50,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:50:50,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:50,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:51,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:50:55,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7dtdc with k8s id: gxy-7dtdc succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:50:55,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 107: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:51:04,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 107 finished +galaxy.model.metadata DEBUG 2024-10-05 06:51:04,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 146 +galaxy.model.metadata DEBUG 2024-10-05 06:51:04,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 147 +galaxy.model.metadata DEBUG 2024-10-05 06:51:04,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 148 +galaxy.model.metadata DEBUG 2024-10-05 06:51:04,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 149 +galaxy.jobs INFO 2024-10-05 06:51:04,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 107 in /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs DEBUG 2024-10-05 06:51:04,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 107 executed (151.649 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:04,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:51:06,530 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 108 +tpv.core.entities DEBUG 2024-10-05 06:51:06,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:51:06,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:51:06,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:51:06,573 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:51:06,588 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Working directory for job is: /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs.runners DEBUG 2024-10-05 06:51:06,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [108] queued (34.463 ms) +galaxy.jobs.handler INFO 2024-10-05 06:51:06,599 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:06,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 108 +galaxy.jobs DEBUG 2024-10-05 06:51:06,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [108] prepared (82.854 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:51:06,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/108/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/108/registry.xml' '/galaxy/server/database/jobs_directory/000/108/upload_params.json' '150:/galaxy/server/database/objects/d/e/6/dataset_de647293-89aa-4a7e-ad0e-7448920b0b17_files:/galaxy/server/database/objects/d/e/6/dataset_de647293-89aa-4a7e-ad0e-7448920b0b17.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:51:06,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (108) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/108/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/108/galaxy_108.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:06,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 108 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:06,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 108 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:07,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:18,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ffrc6 with k8s id: gxy-ffrc6 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:51:18,479 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 108: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:51:27,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 108 finished +galaxy.model.metadata DEBUG 2024-10-05 06:51:27,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 150 +galaxy.jobs INFO 2024-10-05 06:51:27,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 108 in /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs DEBUG 2024-10-05 06:51:27,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 108 executed (96.557 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:27,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 108 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:51:29,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 109 +tpv.core.entities DEBUG 2024-10-05 06:51:29,159 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:51:29,160 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:51:29,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:51:29,176 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:51:29,191 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Working directory for job is: /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs.runners DEBUG 2024-10-05 06:51:29,199 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [109] queued (35.632 ms) +galaxy.jobs.handler INFO 2024-10-05 06:51:29,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:29,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 109 +galaxy.jobs DEBUG 2024-10-05 06:51:29,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [109] prepared (79.030 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:51:29,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/109/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/109/registry.xml' '/galaxy/server/database/jobs_directory/000/109/upload_params.json' '151:/galaxy/server/database/objects/b/6/2/dataset_b624059e-762e-48fc-af23-f38c273ac452_files:/galaxy/server/database/objects/b/6/2/dataset_b624059e-762e-48fc-af23-f38c273ac452.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:51:29,322 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (109) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/109/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/109/galaxy_109.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:29,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 109 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:29,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 109 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:30,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:41,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-k2psz with k8s id: gxy-k2psz succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:51:41,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 109: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:51:50,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 109 finished +galaxy.model.metadata DEBUG 2024-10-05 06:51:51,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 151 +galaxy.jobs INFO 2024-10-05 06:51:51,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 109 in /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs DEBUG 2024-10-05 06:51:51,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 109 executed (121.258 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:51,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 109 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:51:52,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 110 +tpv.core.entities DEBUG 2024-10-05 06:51:52,682 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:51:52,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:51:52,687 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:51:52,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:51:52,713 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Working directory for job is: /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs.runners DEBUG 2024-10-05 06:51:52,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [110] queued (45.203 ms) +galaxy.jobs.handler INFO 2024-10-05 06:51:52,736 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:52,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 110 +galaxy.jobs DEBUG 2024-10-05 06:51:52,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [110] prepared (82.487 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:51:52,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/110/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/110/registry.xml' '/galaxy/server/database/jobs_directory/000/110/upload_params.json' '152:/galaxy/server/database/objects/4/c/4/dataset_4c40c56e-f5b2-4626-820f-9f45d92535e3_files:/galaxy/server/database/objects/4/c/4/dataset_4c40c56e-f5b2-4626-820f-9f45d92535e3.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:51:52,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (110) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/110/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/110/galaxy_110.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:52,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 110 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:52,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 110 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:51:53,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:03,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kb4xs with k8s id: gxy-kb4xs succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:52:03,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 110: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:52:13,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 110 finished +galaxy.model.metadata DEBUG 2024-10-05 06:52:13,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 152 +galaxy.jobs INFO 2024-10-05 06:52:13,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 110 in /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs DEBUG 2024-10-05 06:52:13,187 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 110 executed (106.988 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:13,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 110 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:52:14,148 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 111 +tpv.core.entities DEBUG 2024-10-05 06:52:14,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:52:14,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:52:14,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:52:14,198 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:52:14,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Working directory for job is: /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs.runners DEBUG 2024-10-05 06:52:14,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [111] queued (34.653 ms) +galaxy.jobs.handler INFO 2024-10-05 06:52:14,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:14,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 111 +galaxy.jobs DEBUG 2024-10-05 06:52:14,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [111] prepared (78.777 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:52:14,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/111/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/111/registry.xml' '/galaxy/server/database/jobs_directory/000/111/upload_params.json' '153:/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55_files:/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:52:14,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (111) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/111/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/111/galaxy_111.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:14,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 111 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:14,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 111 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:14,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:52:15,226 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 112 +tpv.core.entities DEBUG 2024-10-05 06:52:15,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:52:15,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:52:15,262 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:52:15,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:52:15,287 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Working directory for job is: /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs.runners DEBUG 2024-10-05 06:52:15,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [112] queued (31.990 ms) +galaxy.jobs.handler INFO 2024-10-05 06:52:15,296 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:15,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 112 +galaxy.jobs DEBUG 2024-10-05 06:52:15,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [112] prepared (81.182 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:52:15,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/112/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/112/registry.xml' '/galaxy/server/database/jobs_directory/000/112/upload_params.json' '154:/galaxy/server/database/objects/c/6/d/dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83_files:/galaxy/server/database/objects/c/6/d/dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:52:15,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (112) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/112/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/112/galaxy_112.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:15,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 112 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:15,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 112 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:15,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:27,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pgsv5 with k8s id: gxy-pgsv5 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:27,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tcmd5 with k8s id: gxy-tcmd5 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:52:27,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 111: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:52:27,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 112: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:52:37,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 111 finished +galaxy.model.metadata DEBUG 2024-10-05 06:52:37,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 153 +galaxy.jobs INFO 2024-10-05 06:52:37,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 111 in /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs.runners DEBUG 2024-10-05 06:52:37,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 112 finished +galaxy.model.metadata DEBUG 2024-10-05 06:52:37,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 154 +galaxy.jobs DEBUG 2024-10-05 06:52:37,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 111 executed (164.646 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:37,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 111 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs INFO 2024-10-05 06:52:37,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 112 in /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs DEBUG 2024-10-05 06:52:37,306 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 112 executed (104.522 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:37,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 112 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:52:37,837 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 113 +tpv.core.entities DEBUG 2024-10-05 06:52:37,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*, abstract=False, cores=2, mem=8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:52:37,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:52:37,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:52:37,886 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:52:37,903 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Working directory for job is: /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs.runners DEBUG 2024-10-05 06:52:37,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [113] queued (38.009 ms) +galaxy.jobs.handler INFO 2024-10-05 06:52:37,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:37,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 113 +galaxy.jobs DEBUG 2024-10-05 06:52:37,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [113] prepared (64.802 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:52:37,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:52:37,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:52:38,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:52:38,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/113/tool_script.sh] for tool command [featureCounts -v 2>&1 | grep . > /galaxy/server/database/jobs_directory/000/113/outputs/COMMAND_VERSION 2>&1; +export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/c/6/d/dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83.dat' -F "GTF" -o "output" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 -R BAM '/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat' && grep -v "^#" "output" | sed -e 's|/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat|subset.sorted.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/0/9/1/dataset_091fa6c5-4727-4678-9eeb-23251579ff2e.dat' && samtools sort --no-PG -o '/galaxy/server/database/objects/9/2/3/dataset_9233b959-c356-4abe-ac56-62607905de86.dat' -@ ${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" *.featureCounts.bam && sed -e 's|/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat|subset.sorted.bam|g' 'output.summary' > '/galaxy/server/database/objects/1/f/b/dataset_1fb806bc-c185-4443-b880-e9f50f36e8e3.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:52:38,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (113) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/113/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/113/galaxy_113.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:38,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 113 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:52:38,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:52:38,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2: mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:52:38,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:80948538a8bdca8b6531966deccf2b5302e3d649-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:38,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 113 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:38,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:42,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-km77j with k8s id: gxy-km77j succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:52:42,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 113: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:52:51,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 113 finished +galaxy.model.metadata DEBUG 2024-10-05 06:52:51,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 155 +galaxy.model.metadata DEBUG 2024-10-05 06:52:51,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 156 +galaxy.model.metadata DEBUG 2024-10-05 06:52:51,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 157 +galaxy.jobs INFO 2024-10-05 06:52:51,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 113 in /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs DEBUG 2024-10-05 06:52:51,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 113 executed (177.028 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:51,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 113 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:52:55,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 114 +tpv.core.entities DEBUG 2024-10-05 06:52:55,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:52:55,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:52:55,288 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:52:55,300 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:52:55,316 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Working directory for job is: /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs.runners DEBUG 2024-10-05 06:52:55,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [114] queued (35.629 ms) +galaxy.jobs.handler INFO 2024-10-05 06:52:55,326 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:55,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 114 +galaxy.jobs DEBUG 2024-10-05 06:52:55,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [114] prepared (80.387 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:52:55,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/114/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/114/registry.xml' '/galaxy/server/database/jobs_directory/000/114/upload_params.json' '158:/galaxy/server/database/objects/0/2/1/dataset_021904c0-913a-4f00-885b-8a114490492e_files:/galaxy/server/database/objects/0/2/1/dataset_021904c0-913a-4f00-885b-8a114490492e.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:52:55,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (114) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/114/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/114/galaxy_114.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:55,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 114 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:55,479 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 114 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:52:56,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:06,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-gmhjt with k8s id: gxy-gmhjt succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:53:06,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 114: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:53:16,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 114 finished +galaxy.model.metadata DEBUG 2024-10-05 06:53:16,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 158 +galaxy.jobs INFO 2024-10-05 06:53:16,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 114 in /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs DEBUG 2024-10-05 06:53:16,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 114 executed (100.672 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:16,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 114 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:53:16,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 115 +tpv.core.entities DEBUG 2024-10-05 06:53:16,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:53:16,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:53:16,819 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:53:16,833 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:53:16,848 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Working directory for job is: /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs.runners DEBUG 2024-10-05 06:53:16,858 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [115] queued (38.893 ms) +galaxy.jobs.handler INFO 2024-10-05 06:53:16,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:16,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 115 +galaxy.tools.wrappers WARNING 2024-10-05 06:53:16,909 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-10-05 06:53:16,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [115] prepared (51.641 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:53:16,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:53:16,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:53:17,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:53:17,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/115/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/115/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/0/2/1/dataset_021904c0-913a-4f00-885b-8a114490492e.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/0/f/c/dataset_0fc7fba4-540b-4320-94e0-36425cebda0a.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:53:17,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (115) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/115/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/115/galaxy_115.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:17,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 115 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:53:17,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:53:17,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:53:17,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:17,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 115 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:17,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:24,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-mtf45 with k8s id: gxy-mtf45 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:53:25,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 115: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:53:34,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 115 finished +galaxy.model.metadata DEBUG 2024-10-05 06:53:34,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 159 +galaxy.jobs INFO 2024-10-05 06:53:34,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 115 in /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs DEBUG 2024-10-05 06:53:34,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 115 executed (101.777 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:34,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 115 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:53:36,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 116 +tpv.core.entities DEBUG 2024-10-05 06:53:36,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:53:36,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:53:36,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:53:36,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:53:36,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Working directory for job is: /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs.runners DEBUG 2024-10-05 06:53:36,332 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [116] queued (36.088 ms) +galaxy.jobs.handler INFO 2024-10-05 06:53:36,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:36,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 116 +galaxy.jobs DEBUG 2024-10-05 06:53:36,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [116] prepared (79.127 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:53:36,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/116/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/116/registry.xml' '/galaxy/server/database/jobs_directory/000/116/upload_params.json' '160:/galaxy/server/database/objects/5/5/8/dataset_55886639-e887-4ce9-a9d5-0619bc31ea48_files:/galaxy/server/database/objects/5/5/8/dataset_55886639-e887-4ce9-a9d5-0619bc31ea48.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:53:36,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (116) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/116/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/116/galaxy_116.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:36,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:36,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:36,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-nlk7h failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-nlk7h. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:53:47,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-nlk7h + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-nlk7h": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (116/gxy-nlk7h) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (116/gxy-nlk7h) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (116/gxy-nlk7h) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (116/gxy-nlk7h) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-nlk7h. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 116 (gxy-nlk7h) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-nlk7h to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:47,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (116/gxy-nlk7h) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-10-05 06:53:48,568 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 117 +tpv.core.entities DEBUG 2024-10-05 06:53:48,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:53:48,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:53:48,600 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:53:48,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:53:48,624 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Working directory for job is: /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs.runners DEBUG 2024-10-05 06:53:48,632 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [117] queued (32.133 ms) +galaxy.jobs.handler INFO 2024-10-05 06:53:48,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:48,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 117 +galaxy.jobs DEBUG 2024-10-05 06:53:48,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [117] prepared (76.581 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:53:48,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/117/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/117/registry.xml' '/galaxy/server/database/jobs_directory/000/117/upload_params.json' '161:/galaxy/server/database/objects/a/4/2/dataset_a427b668-df70-4d93-bf0d-7e8f425d70f4_files:/galaxy/server/database/objects/a/4/2/dataset_a427b668-df70-4d93-bf0d-7e8f425d70f4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:53:48,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (117) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/117/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/117/galaxy_117.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:48,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 117 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:48,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 117 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:53:49,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:00,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-b25vc with k8s id: gxy-b25vc succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:54:00,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 117: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:54:09,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 117 finished +galaxy.model.metadata DEBUG 2024-10-05 06:54:09,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 161 +galaxy.jobs INFO 2024-10-05 06:54:09,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 117 in /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs DEBUG 2024-10-05 06:54:09,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 117 executed (100.657 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:09,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 117 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:54:10,040 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 118 +tpv.core.entities DEBUG 2024-10-05 06:54:10,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:54:10,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:54:10,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:54:10,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:54:10,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Working directory for job is: /galaxy/server/database/jobs_directory/000/118 +galaxy.jobs.runners DEBUG 2024-10-05 06:54:10,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [118] queued (39.677 ms) +galaxy.jobs.handler INFO 2024-10-05 06:54:10,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:10,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 118 +galaxy.tools.wrappers WARNING 2024-10-05 06:54:10,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-10-05 06:54:10,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [118] prepared (44.797 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:10,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:54:10,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:10,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:54:10,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/118/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/118/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/a/4/2/dataset_a427b668-df70-4d93-bf0d-7e8f425d70f4.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/e/6/2/dataset_e62778dc-6e69-4eec-bae3-03bd673dd5f0.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:54:10,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (118) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/118/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/118/galaxy_118.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:10,526 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:10,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:54:10,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:10,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:10,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:11,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-k9dxb failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-k9dxb. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 06:54:14,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-k9dxb + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-k9dxb": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (118/gxy-k9dxb) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (118/gxy-k9dxb) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (118/gxy-k9dxb) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (118/gxy-k9dxb) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-k9dxb. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Attempting to stop job 118 (gxy-k9dxb) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Found job with id gxy-k9dxb to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:14,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (118/gxy-k9dxb) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-10-05 06:54:16,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 119 +tpv.core.entities DEBUG 2024-10-05 06:54:16,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:54:16,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:54:16,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:54:16,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:54:16,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Working directory for job is: /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs.runners DEBUG 2024-10-05 06:54:16,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [119] queued (34.765 ms) +galaxy.jobs.handler INFO 2024-10-05 06:54:16,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:16,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 119 +galaxy.jobs DEBUG 2024-10-05 06:54:16,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [119] prepared (79.860 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:54:16,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/119/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/119/registry.xml' '/galaxy/server/database/jobs_directory/000/119/upload_params.json' '163:/galaxy/server/database/objects/8/8/f/dataset_88f29a04-a065-490d-91b7-5bdb43eaaca4_files:/galaxy/server/database/objects/8/8/f/dataset_88f29a04-a065-490d-91b7-5bdb43eaaca4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:54:16,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (119) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/119/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/119/galaxy_119.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:16,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 119 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:16,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 119 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:16,780 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:27,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-79phx with k8s id: gxy-79phx succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:54:28,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 119: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:54:37,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 119 finished +galaxy.model.metadata DEBUG 2024-10-05 06:54:37,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 163 +galaxy.jobs INFO 2024-10-05 06:54:37,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 119 in /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs DEBUG 2024-10-05 06:54:37,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 119 executed (98.691 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:37,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 119 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:54:37,711 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 120 +tpv.core.entities DEBUG 2024-10-05 06:54:37,745 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:54:37,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:54:37,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:54:37,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:54:37,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Working directory for job is: /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs.runners DEBUG 2024-10-05 06:54:37,782 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [120] queued (31.930 ms) +galaxy.jobs.handler INFO 2024-10-05 06:54:37,784 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:37,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 120 +galaxy.tools.wrappers WARNING 2024-10-05 06:54:37,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-10-05 06:54:37,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [120] prepared (43.686 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:37,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:54:37,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:37,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:54:37,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/120/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/120/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/8/8/f/dataset_88f29a04-a065-490d-91b7-5bdb43eaaca4.dat' && samtools fixmate -@ $addthreads -c -O BAM namesorted.bam '/galaxy/server/database/objects/0/f/9/dataset_0f94ec1b-b461-4672-8f47-3478389d051c.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:54:37,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (120) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/120/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/120/galaxy_120.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:37,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 120 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:37,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:54:37,927 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:54:37,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:37,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 120 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:38,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:42,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9pfbh with k8s id: gxy-9pfbh succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:54:42,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 120: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:54:51,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 120 finished +galaxy.model.metadata DEBUG 2024-10-05 06:54:51,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 164 +galaxy.jobs INFO 2024-10-05 06:54:51,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 120 in /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs DEBUG 2024-10-05 06:54:51,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 120 executed (103.591 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:51,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 120 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:54:52,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 121 +tpv.core.entities DEBUG 2024-10-05 06:54:52,095 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:54:52,096 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:54:52,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:54:52,114 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:54:52,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Working directory for job is: /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs.runners DEBUG 2024-10-05 06:54:52,136 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [121] queued (35.210 ms) +galaxy.jobs.handler INFO 2024-10-05 06:54:52,138 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:52,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 121 +galaxy.jobs DEBUG 2024-10-05 06:54:52,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [121] prepared (82.779 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:54:52,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/121/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/121/registry.xml' '/galaxy/server/database/jobs_directory/000/121/upload_params.json' '165:/galaxy/server/database/objects/6/1/8/dataset_618c9a63-ac93-4f05-a06b-80f31cb7b90d_files:/galaxy/server/database/objects/6/1/8/dataset_618c9a63-ac93-4f05-a06b-80f31cb7b90d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:54:52,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (121) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/121/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/121/galaxy_121.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:52,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 121 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:52,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 121 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:54:53,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:04,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-n88w9 with k8s id: gxy-n88w9 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:55:04,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 121: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:55:13,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 121 finished +galaxy.model.metadata DEBUG 2024-10-05 06:55:13,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 165 +galaxy.jobs INFO 2024-10-05 06:55:13,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 121 in /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs DEBUG 2024-10-05 06:55:13,667 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 121 executed (116.271 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:13,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 121 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:55:14,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 122 +tpv.core.entities DEBUG 2024-10-05 06:55:14,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:55:14,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:55:14,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:55:14,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:55:14,641 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Working directory for job is: /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs.runners DEBUG 2024-10-05 06:55:14,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [122] queued (34.240 ms) +galaxy.jobs.handler INFO 2024-10-05 06:55:14,653 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:14,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 122 +galaxy.tools.wrappers WARNING 2024-10-05 06:55:14,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-10-05 06:55:14,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [122] prepared (45.168 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:14,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:55:14,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:14,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:55:14,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/122/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/122/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/6/1/8/dataset_618c9a63-ac93-4f05-a06b-80f31cb7b90d.dat' && samtools fixmate -@ $addthreads -c -O BAM namesorted.bam '/galaxy/server/database/objects/e/f/f/dataset_effb724b-b92f-47fd-936f-5ffe87d686b9.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:55:14,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (122) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/122/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/122/galaxy_122.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:14,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 122 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:14,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:55:14,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:14,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:14,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 122 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:15,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:19,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ckslq with k8s id: gxy-ckslq succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:55:19,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 122: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:55:28,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 122 finished +galaxy.model.metadata DEBUG 2024-10-05 06:55:28,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 166 +galaxy.jobs INFO 2024-10-05 06:55:28,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 122 in /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs DEBUG 2024-10-05 06:55:28,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 122 executed (86.867 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:28,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 122 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:55:30,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 123 +tpv.core.entities DEBUG 2024-10-05 06:55:30,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:55:30,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:55:30,150 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:55:30,162 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:55:30,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Working directory for job is: /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs.runners DEBUG 2024-10-05 06:55:30,182 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [123] queued (31.701 ms) +galaxy.jobs.handler INFO 2024-10-05 06:55:30,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:30,187 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 123 +galaxy.jobs DEBUG 2024-10-05 06:55:30,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [123] prepared (102.535 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:55:30,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/123/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/123/registry.xml' '/galaxy/server/database/jobs_directory/000/123/upload_params.json' '167:/galaxy/server/database/objects/0/4/1/dataset_0419d18d-a71c-4bc9-938b-7e0430cf305d_files:/galaxy/server/database/objects/0/4/1/dataset_0419d18d-a71c-4bc9-938b-7e0430cf305d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:55:30,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (123) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/123/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/123/galaxy_123.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:30,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 123 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:30,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 123 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:31,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:41,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-v4zc2 with k8s id: gxy-v4zc2 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:55:41,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 123: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:55:50,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 123 finished +galaxy.model.metadata DEBUG 2024-10-05 06:55:50,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 167 +galaxy.jobs INFO 2024-10-05 06:55:50,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 123 in /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs DEBUG 2024-10-05 06:55:50,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 123 executed (106.608 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:50,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 123 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:55:51,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 124 +tpv.core.entities DEBUG 2024-10-05 06:55:51,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:55:51,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:55:51,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:55:51,656 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:55:51,670 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Working directory for job is: /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs.runners DEBUG 2024-10-05 06:55:51,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [124] queued (35.641 ms) +galaxy.jobs.handler INFO 2024-10-05 06:55:51,682 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:51,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 124 +galaxy.tools.wrappers WARNING 2024-10-05 06:55:51,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-10-05 06:55:51,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [124] prepared (44.270 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:51,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:55:51,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:51,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:55:51,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/124/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/124/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/0/4/1/dataset_0419d18d-a71c-4bc9-938b-7e0430cf305d.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/e/d/c/dataset_edc879ec-6fac-4210-af05-46c4a19297ae.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:55:51,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (124) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/124/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/124/galaxy_124.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:51,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 124 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:51,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:55:51,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:55:51,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:51,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 124 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:52,569 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:55:56,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8jgs2 with k8s id: gxy-8jgs2 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:55:56,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 124: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:56:06,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 124 finished +galaxy.model.metadata DEBUG 2024-10-05 06:56:06,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 168 +galaxy.jobs INFO 2024-10-05 06:56:06,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 124 in /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs DEBUG 2024-10-05 06:56:06,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 124 executed (101.903 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:06,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 124 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:56:08,004 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 125 +tpv.core.entities DEBUG 2024-10-05 06:56:08,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:56:08,034 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:56:08,038 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:56:08,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:56:08,066 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Working directory for job is: /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs.runners DEBUG 2024-10-05 06:56:08,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [125] queued (35.437 ms) +galaxy.jobs.handler INFO 2024-10-05 06:56:08,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:08,078 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 125 +galaxy.jobs DEBUG 2024-10-05 06:56:08,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [125] prepared (78.354 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:56:08,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/125/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/125/registry.xml' '/galaxy/server/database/jobs_directory/000/125/upload_params.json' '169:/galaxy/server/database/objects/7/3/d/dataset_73dcba4f-567f-48cc-a717-1fe260b4c91f_files:/galaxy/server/database/objects/7/3/d/dataset_73dcba4f-567f-48cc-a717-1fe260b4c91f.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:56:08,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (125) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/125/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/125/galaxy_125.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:08,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 125 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:08,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 125 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:08,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:56:09,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 126 +tpv.core.entities DEBUG 2024-10-05 06:56:09,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:56:09,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:56:09,113 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:56:09,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:56:09,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Working directory for job is: /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs.runners DEBUG 2024-10-05 06:56:09,144 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [126] queued (31.352 ms) +galaxy.jobs.handler INFO 2024-10-05 06:56:09,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:09,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 126 +galaxy.jobs DEBUG 2024-10-05 06:56:09,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [126] prepared (72.059 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:56:09,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/126/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/126/registry.xml' '/galaxy/server/database/jobs_directory/000/126/upload_params.json' '170:/galaxy/server/database/objects/d/8/8/dataset_d88f636c-feab-4fa9-bb74-50b75eda92f3_files:/galaxy/server/database/objects/d/8/8/dataset_d88f636c-feab-4fa9-bb74-50b75eda92f3.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:56:09,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (126) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/126/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/126/galaxy_126.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:09,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 126 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:09,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 126 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:09,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:18,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8rwwg with k8s id: gxy-8rwwg succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:56:19,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 125: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:21,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hqhpb with k8s id: gxy-hqhpb succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:56:21,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 126: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:56:28,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 125 finished +galaxy.model.metadata DEBUG 2024-10-05 06:56:28,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 169 +galaxy.jobs INFO 2024-10-05 06:56:28,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 125 in /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs DEBUG 2024-10-05 06:56:28,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 125 executed (102.134 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:28,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 125 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:56:30,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 126 finished +galaxy.model.metadata DEBUG 2024-10-05 06:56:30,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 170 +galaxy.jobs INFO 2024-10-05 06:56:30,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 126 in /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs DEBUG 2024-10-05 06:56:30,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 126 executed (105.587 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:30,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 126 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:56:31,598 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 127 +tpv.core.entities DEBUG 2024-10-05 06:56:31,633 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:56:31,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:56:31,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:56:31,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:56:31,666 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Working directory for job is: /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs.runners DEBUG 2024-10-05 06:56:31,675 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [127] queued (36.505 ms) +galaxy.jobs.handler INFO 2024-10-05 06:56:31,677 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:31,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 127 +galaxy.jobs DEBUG 2024-10-05 06:56:31,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [127] prepared (59.274 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:56:31,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:56:31,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:56:31,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:56:31,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/127/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/127/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/d/8/8/dataset_d88f636c-feab-4fa9-bb74-50b75eda92f3.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/7/3/d/dataset_73dcba4f-567f-48cc-a717-1fe260b4c91f.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/0/3/d/dataset_03db1fa2-8b8a-424d-927d-f347f50c4aca.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-10-05 06:56:31,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (127) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/127/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/127/galaxy_127.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:31,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 127 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:56:31,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:56:31,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:56:31,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:31,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 127 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:32,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:39,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-jbhxx with k8s id: gxy-jbhxx succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:56:39,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 127: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:56:48,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 127 finished +galaxy.model.metadata DEBUG 2024-10-05 06:56:48,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 171 +galaxy.jobs INFO 2024-10-05 06:56:48,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 127 in /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs DEBUG 2024-10-05 06:56:48,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 127 executed (102.081 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:48,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 127 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:56:50,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 129, 128 +tpv.core.entities DEBUG 2024-10-05 06:56:50,059 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:56:50,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:56:50,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:56:50,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:56:50,094 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Working directory for job is: /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs.runners DEBUG 2024-10-05 06:56:50,101 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [128] queued (36.233 ms) +galaxy.jobs.handler INFO 2024-10-05 06:56:50,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:50,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 128 +tpv.core.entities DEBUG 2024-10-05 06:56:50,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:56:50,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:56:50,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:56:50,134 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:56:50,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Working directory for job is: /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs.runners DEBUG 2024-10-05 06:56:50,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [129] queued (50.827 ms) +galaxy.jobs.handler INFO 2024-10-05 06:56:50,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:50,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 129 +galaxy.jobs DEBUG 2024-10-05 06:56:50,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [128] prepared (94.957 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:56:50,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/128/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/128/registry.xml' '/galaxy/server/database/jobs_directory/000/128/upload_params.json' '172:/galaxy/server/database/objects/5/6/d/dataset_56dc444b-693d-4f3b-8e1d-88c617b97041_files:/galaxy/server/database/objects/5/6/d/dataset_56dc444b-693d-4f3b-8e1d-88c617b97041.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:56:50,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (128) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/128/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/128/galaxy_128.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:56:50,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [129] prepared (133.050 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:50,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 128 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:56:50,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/129/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/129/registry.xml' '/galaxy/server/database/jobs_directory/000/129/upload_params.json' '173:/galaxy/server/database/objects/8/c/8/dataset_8c8c3583-fd8f-479a-9e2a-d4cd04114513_files:/galaxy/server/database/objects/8/c/8/dataset_8c8c3583-fd8f-479a-9e2a-d4cd04114513.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:56:50,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (129) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/129/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/129/galaxy_129.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:50,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 128 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:50,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 129 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:50,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 129 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:51,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:56:51,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:02,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pxtm9 with k8s id: gxy-pxtm9 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:02,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-x9rnv with k8s id: gxy-x9rnv succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:57:02,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 128: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:57:02,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 129: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:57:12,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 129 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:57:12,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 128 finished +galaxy.model.metadata DEBUG 2024-10-05 06:57:12,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 173 +galaxy.model.metadata DEBUG 2024-10-05 06:57:12,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 172 +galaxy.jobs INFO 2024-10-05 06:57:12,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 129 in /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs INFO 2024-10-05 06:57:12,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 128 in /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs DEBUG 2024-10-05 06:57:12,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 129 executed (117.639 ms) +galaxy.jobs DEBUG 2024-10-05 06:57:12,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 128 executed (117.174 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:12,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 129 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:12,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 128 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:57:13,720 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 130 +tpv.core.entities DEBUG 2024-10-05 06:57:13,752 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:57:13,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:57:13,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:57:13,770 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:57:13,784 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Working directory for job is: /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs.runners DEBUG 2024-10-05 06:57:13,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [130] queued (35.325 ms) +galaxy.jobs.handler INFO 2024-10-05 06:57:13,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:13,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 130 +galaxy.jobs DEBUG 2024-10-05 06:57:13,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [130] prepared (46.808 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:13,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:57:13,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:13,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:57:13,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/130/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/130/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/8/c/8/dataset_8c8c3583-fd8f-479a-9e2a-d4cd04114513.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/5/6/d/dataset_56dc444b-693d-4f3b-8e1d-88c617b97041.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/d/c/9/dataset_dc955291-da99-4d52-96ae-58f74564d12f.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-10-05 06:57:13,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (130) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/130/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/130/galaxy_130.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:13,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:13,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:57:13,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:13,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:13,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:14,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:18,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9vzd6 with k8s id: gxy-9vzd6 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:57:18,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 130: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:57:28,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 130 finished +galaxy.model.metadata DEBUG 2024-10-05 06:57:28,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 174 +galaxy.jobs INFO 2024-10-05 06:57:28,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 130 in /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs DEBUG 2024-10-05 06:57:28,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 130 executed (105.187 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:28,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:57:30,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 132, 131 +tpv.core.entities DEBUG 2024-10-05 06:57:30,135 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:57:30,135 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:57:30,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:57:30,152 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:57:30,165 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Working directory for job is: /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs.runners DEBUG 2024-10-05 06:57:30,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [131] queued (32.693 ms) +galaxy.jobs.handler INFO 2024-10-05 06:57:30,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 131 +tpv.core.entities DEBUG 2024-10-05 06:57:30,187 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:57:30,188 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:57:30,192 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:57:30,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:57:30,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Working directory for job is: /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs.runners DEBUG 2024-10-05 06:57:30,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [132] queued (47.570 ms) +galaxy.jobs.handler INFO 2024-10-05 06:57:30,270 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 132 +galaxy.jobs DEBUG 2024-10-05 06:57:30,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [131] prepared (121.855 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:57:30,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/131/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/131/registry.xml' '/galaxy/server/database/jobs_directory/000/131/upload_params.json' '175:/galaxy/server/database/objects/0/4/8/dataset_048413cc-110a-4e4d-9aec-dd677dce85e9_files:/galaxy/server/database/objects/0/4/8/dataset_048413cc-110a-4e4d-9aec-dd677dce85e9.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:57:30,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (131) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/131/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/131/galaxy_131.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:57:30,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [132] prepared (106.344 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 131 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 131 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:57:30,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/132/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/132/registry.xml' '/galaxy/server/database/jobs_directory/000/132/upload_params.json' '176:/galaxy/server/database/objects/e/0/5/dataset_e05679a2-fbbf-41c1-945a-3ba7592ba7fe_files:/galaxy/server/database/objects/e/0/5/dataset_e05679a2-fbbf-41c1-945a-3ba7592ba7fe.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:57:30,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (132) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/132/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/132/galaxy_132.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 132 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 132 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:30,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:31,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:42,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zzqtk with k8s id: gxy-zzqtk succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:42,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4k76k with k8s id: gxy-4k76k succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:57:42,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 131: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:57:42,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 132: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:57:52,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 131 finished +galaxy.model.metadata DEBUG 2024-10-05 06:57:52,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 175 +galaxy.jobs INFO 2024-10-05 06:57:52,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 131 in /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs DEBUG 2024-10-05 06:57:52,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 131 executed (104.324 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:52,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 131 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:57:52,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 132 finished +galaxy.model.metadata DEBUG 2024-10-05 06:57:52,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 176 +galaxy.jobs INFO 2024-10-05 06:57:52,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 132 in /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs DEBUG 2024-10-05 06:57:52,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 132 executed (89.188 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:52,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 132 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:57:52,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 133 +tpv.core.entities DEBUG 2024-10-05 06:57:52,872 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:57:52,873 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:57:52,877 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:57:52,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:57:52,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Working directory for job is: /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs.runners DEBUG 2024-10-05 06:57:52,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [133] queued (35.256 ms) +galaxy.jobs.handler INFO 2024-10-05 06:57:52,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:52,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 133 +galaxy.jobs DEBUG 2024-10-05 06:57:52,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [133] prepared (50.563 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:52,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:57:52,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:53,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:57:53,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/133/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/133/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa.gz" && ln -s '/galaxy/server/database/objects/e/0/5/dataset_e05679a2-fbbf-41c1-945a-3ba7592ba7fe.dat' $reffa && { samtools faidx $reffa || { echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 && gzip -dc $reffa > reference.fa && reffa="reference.fa" && samtools faidx $reffa; } } && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/0/4/8/dataset_048413cc-110a-4e4d-9aec-dd677dce85e9.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/7/4/e/dataset_74e79f05-0234-4860-b882-84a78ecc84cc.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-10-05 06:57:53,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (133) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/133/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/133/galaxy_133.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:53,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 133 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:53,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:57:53,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:57:53,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:53,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 133 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:53,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:57:57,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-d4l9k with k8s id: gxy-d4l9k succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:57:57,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 133: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:58:06,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 133 finished +galaxy.model.metadata DEBUG 2024-10-05 06:58:06,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 177 +galaxy.jobs INFO 2024-10-05 06:58:06,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 133 in /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs DEBUG 2024-10-05 06:58:06,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 133 executed (109.297 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:06,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 133 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:58:08,203 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 135, 134 +tpv.core.entities DEBUG 2024-10-05 06:58:08,231 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:58:08,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:58:08,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:58:08,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:58:08,262 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Working directory for job is: /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs.runners DEBUG 2024-10-05 06:58:08,270 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [134] queued (34.257 ms) +galaxy.jobs.handler INFO 2024-10-05 06:58:08,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:08,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 134 +tpv.core.entities DEBUG 2024-10-05 06:58:08,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:58:08,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:58:08,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:58:08,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:58:08,327 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Working directory for job is: /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs.runners DEBUG 2024-10-05 06:58:08,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [135] queued (44.741 ms) +galaxy.jobs.handler INFO 2024-10-05 06:58:08,339 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:08,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 135 +galaxy.jobs DEBUG 2024-10-05 06:58:08,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [134] prepared (100.304 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:58:08,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/134/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/134/registry.xml' '/galaxy/server/database/jobs_directory/000/134/upload_params.json' '178:/galaxy/server/database/objects/d/6/1/dataset_d618c816-154b-47d3-9668-e8edbe6edaa5_files:/galaxy/server/database/objects/d/6/1/dataset_d618c816-154b-47d3-9668-e8edbe6edaa5.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:58:08,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (134) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/134/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/134/galaxy_134.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 06:58:08,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [135] prepared (83.583 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:08,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 134 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:08,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 134 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 06:58:08,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/135/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/135/registry.xml' '/galaxy/server/database/jobs_directory/000/135/upload_params.json' '179:/galaxy/server/database/objects/b/6/c/dataset_b6ca7d7d-f4c8-4027-8d87-8a9b790933e1_files:/galaxy/server/database/objects/b/6/c/dataset_b6ca7d7d-f4c8-4027-8d87-8a9b790933e1.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:58:08,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (135) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/135/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/135/galaxy_135.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:08,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:08,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:09,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:09,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:19,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-nlp7d with k8s id: gxy-nlp7d succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:19,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-jv4bh with k8s id: gxy-jv4bh succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:58:19,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 134: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:58:19,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 135: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:58:29,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 134 finished +galaxy.jobs.runners DEBUG 2024-10-05 06:58:29,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 135 finished +galaxy.model.metadata DEBUG 2024-10-05 06:58:29,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 178 +galaxy.model.metadata DEBUG 2024-10-05 06:58:29,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 179 +galaxy.jobs INFO 2024-10-05 06:58:29,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 134 in /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs INFO 2024-10-05 06:58:29,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 135 in /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs DEBUG 2024-10-05 06:58:29,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 134 executed (131.502 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:29,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 134 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 06:58:29,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 135 executed (123.065 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:29,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:58:31,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 136 +tpv.core.entities DEBUG 2024-10-05 06:58:31,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:58:31,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:58:31,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:58:31,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:58:31,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Working directory for job is: /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs.runners DEBUG 2024-10-05 06:58:31,091 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [136] queued (35.262 ms) +galaxy.jobs.handler INFO 2024-10-05 06:58:31,094 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:31,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 136 +galaxy.jobs DEBUG 2024-10-05 06:58:31,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [136] prepared (52.262 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:58:31,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:58:31,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:58:31,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:58:31,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/136/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/136/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa.gz" && ln -s '/galaxy/server/database/objects/b/6/c/dataset_b6ca7d7d-f4c8-4027-8d87-8a9b790933e1.dat' $reffa && { samtools faidx $reffa || { echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 && gzip -dc $reffa > reference.fa && reffa="reference.fa" && samtools faidx $reffa; } } && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/d/6/1/dataset_d618c816-154b-47d3-9668-e8edbe6edaa5.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/8/b/b/dataset_8bb5f443-8075-45a4-b2e6-f190fb9f27e2.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-10-05 06:58:31,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (136) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/136/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/136/galaxy_136.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:31,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 136 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:58:31,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:58:31,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-10-05 06:58:31,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:31,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 136 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:31,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:35,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-bdrmr with k8s id: gxy-bdrmr succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:58:36,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 136: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:58:45,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 136 finished +galaxy.model.metadata DEBUG 2024-10-05 06:58:45,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 180 +galaxy.jobs INFO 2024-10-05 06:58:45,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 136 in /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs DEBUG 2024-10-05 06:58:45,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 136 executed (104.125 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:45,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 136 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:58:47,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 137 +tpv.core.entities DEBUG 2024-10-05 06:58:47,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:58:47,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:58:47,583 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:58:47,595 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:58:47,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Working directory for job is: /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs.runners DEBUG 2024-10-05 06:58:47,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [137] queued (35.519 ms) +galaxy.jobs.handler INFO 2024-10-05 06:58:47,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:47,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 137 +galaxy.jobs DEBUG 2024-10-05 06:58:47,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [137] prepared (77.477 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:58:47,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/137/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/137/registry.xml' '/galaxy/server/database/jobs_directory/000/137/upload_params.json' '181:/galaxy/server/database/objects/0/6/0/dataset_060a8a6a-4362-444f-88bf-bd3b37622bfb_files:/galaxy/server/database/objects/0/6/0/dataset_060a8a6a-4362-444f-88bf-bd3b37622bfb.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:58:47,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (137) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/137/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/137/galaxy_137.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:47,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:47,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:48,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 06:58:48,625 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 138 +tpv.core.entities DEBUG 2024-10-05 06:58:48,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:58:48,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:58:48,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:58:48,671 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:58:48,685 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Working directory for job is: /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs.runners DEBUG 2024-10-05 06:58:48,692 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [138] queued (33.185 ms) +galaxy.jobs.handler INFO 2024-10-05 06:58:48,695 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:48,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 138 +galaxy.jobs DEBUG 2024-10-05 06:58:48,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [138] prepared (74.102 ms) +galaxy.jobs.command_factory INFO 2024-10-05 06:58:48,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/138/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/138/registry.xml' '/galaxy/server/database/jobs_directory/000/138/upload_params.json' '182:/galaxy/server/database/objects/9/9/2/dataset_992c6633-79b6-4f25-bf14-a64c675c5571_files:/galaxy/server/database/objects/9/9/2/dataset_992c6633-79b6-4f25-bf14-a64c675c5571.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:58:48,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (138) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/138/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/138/galaxy_138.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:48,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 138 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:48,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 138 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:49,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:58:59,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kwmxz with k8s id: gxy-kwmxz succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:58:59,423 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 137: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:00,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-sb8bl with k8s id: gxy-sb8bl succeeded +galaxy.jobs.runners DEBUG 2024-10-05 06:59:00,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 138: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 06:59:09,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 137 finished +galaxy.model.metadata DEBUG 2024-10-05 06:59:09,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 181 +galaxy.jobs INFO 2024-10-05 06:59:09,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 137 in /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs DEBUG 2024-10-05 06:59:09,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 137 executed (104.704 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:09,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 06:59:09,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 138 finished +galaxy.model.metadata DEBUG 2024-10-05 06:59:09,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 182 +galaxy.jobs INFO 2024-10-05 06:59:09,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 138 in /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs DEBUG 2024-10-05 06:59:10,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 138 executed (104.777 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:10,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 138 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 06:59:10,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 139 +tpv.core.entities DEBUG 2024-10-05 06:59:10,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 06:59:10,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 06:59:10,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 06:59:10,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 06:59:10,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Working directory for job is: /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs.runners DEBUG 2024-10-05 06:59:10,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [139] queued (58.475 ms) +galaxy.jobs.handler INFO 2024-10-05 06:59:10,518 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:10,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 139 +cheetah_DynamicallyCompiledCheetahTemplate_1728111550_586365_77514.py:89: SyntaxWarning: invalid escape sequence '\w' +cheetah_DynamicallyCompiledCheetahTemplate_1728111550_586365_77514.py:90: SyntaxWarning: invalid escape sequence '\w' +galaxy.jobs DEBUG 2024-10-05 06:59:10,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [139] prepared (75.930 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 06:59:10,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:59:10,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1: chromeister:1.5.a +galaxy.tool_util.deps.containers INFO 2024-10-05 06:59:10,821 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/chromeister:1.5.a--h031d066_5,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 06:59:10,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/139/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/0/6/0/dataset_060a8a6a-4362-444f-88bf-bd3b37622bfb.dat 'mycoplasma-232.fasta' && ln -s /galaxy/server/database/objects/9/9/2/dataset_992c6633-79b6-4f25-bf14-a64c675c5571.dat 'mycoplasma-7422.fasta' && CHROMEISTER -query 'mycoplasma-232.fasta' -db 'mycoplasma-7422.fasta' -dimension 500 -kmer 32 -diffuse 4 -out 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat && compute_score.R 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat 500 > '/galaxy/server/database/objects/e/2/d/dataset_e2df7c53-b5ef-4548-a518-6a5216251fa5.dat' && detect_events.py 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.raw.txt png && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.png '/galaxy/server/database/objects/d/b/4/dataset_db4131c0-9670-4c36-a016-da97cdfdf309.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat '/galaxy/server/database/objects/2/2/7/dataset_227fbfba-b5be-49cb-a187-8abbf7046cb3.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.filt.png '/galaxy/server/database/objects/2/6/3/dataset_2639f1bc-4384-4349-89f5-060be0dfac05.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.txt '/galaxy/server/database/objects/1/e/1/dataset_1e152f50-87d2-4f1f-85e1-b231ebd5e220.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.csv '/galaxy/server/database/objects/c/6/9/dataset_c69000eb-49b1-47da-ab6c-eb5d7c79c0d8.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 06:59:10,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (139) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/139/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/139/galaxy_139.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:10,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 139 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 06:59:10,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 06:59:10,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1: chromeister:1.5.a +galaxy.tool_util.deps.containers INFO 2024-10-05 06:59:10,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/chromeister:1.5.a--h031d066_5,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:10,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 139 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 06:59:11,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:09,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-sxf2c with k8s id: gxy-sxf2c succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:00:09,537 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 139: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:00:18,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 139 finished +galaxy.model.metadata DEBUG 2024-10-05 07:00:18,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 183 +galaxy.model.metadata DEBUG 2024-10-05 07:00:19,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 184 +galaxy.model.metadata DEBUG 2024-10-05 07:00:19,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 185 +galaxy.model.metadata DEBUG 2024-10-05 07:00:19,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 186 +galaxy.model.metadata DEBUG 2024-10-05 07:00:19,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 187 +galaxy.model.metadata DEBUG 2024-10-05 07:00:19,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 188 +galaxy.util WARNING 2024-10-05 07:00:19,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/2/2/7/dataset_227fbfba-b5be-49cb-a187-8abbf7046cb3.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/2/2/7/dataset_227fbfba-b5be-49cb-a187-8abbf7046cb3.dat' +galaxy.util WARNING 2024-10-05 07:00:19,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/2/6/3/dataset_2639f1bc-4384-4349-89f5-060be0dfac05.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/2/6/3/dataset_2639f1bc-4384-4349-89f5-060be0dfac05.dat' +galaxy.util WARNING 2024-10-05 07:00:19,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/6/9/dataset_c69000eb-49b1-47da-ab6c-eb5d7c79c0d8.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/6/9/dataset_c69000eb-49b1-47da-ab6c-eb5d7c79c0d8.dat' +galaxy.util WARNING 2024-10-05 07:00:19,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/e/1/dataset_1e152f50-87d2-4f1f-85e1-b231ebd5e220.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/e/1/dataset_1e152f50-87d2-4f1f-85e1-b231ebd5e220.dat' +galaxy.util WARNING 2024-10-05 07:00:19,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/d/b/4/dataset_db4131c0-9670-4c36-a016-da97cdfdf309.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/d/b/4/dataset_db4131c0-9670-4c36-a016-da97cdfdf309.dat' +galaxy.jobs INFO 2024-10-05 07:00:19,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 139 in /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs DEBUG 2024-10-05 07:00:19,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 139 executed (175.337 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:19,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 139 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:00:21,979 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 140 +tpv.core.entities DEBUG 2024-10-05 07:00:22,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:00:22,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:00:22,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:00:22,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:00:22,039 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Working directory for job is: /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs.runners DEBUG 2024-10-05 07:00:22,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [140] queued (33.152 ms) +galaxy.jobs.handler INFO 2024-10-05 07:00:22,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:22,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 140 +galaxy.jobs DEBUG 2024-10-05 07:00:22,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [140] prepared (83.523 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:00:22,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/140/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/140/registry.xml' '/galaxy/server/database/jobs_directory/000/140/upload_params.json' '189:/galaxy/server/database/objects/2/9/0/dataset_29085765-63a5-45ce-af65-700da8961e1b_files:/galaxy/server/database/objects/2/9/0/dataset_29085765-63a5-45ce-af65-700da8961e1b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:00:22,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (140) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/140/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/140/galaxy_140.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:22,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 140 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:22,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 140 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:22,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 07:00:23,052 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 141 +tpv.core.entities DEBUG 2024-10-05 07:00:23,081 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:00:23,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:00:23,086 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:00:23,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:00:23,112 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Working directory for job is: /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs.runners DEBUG 2024-10-05 07:00:23,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [141] queued (33.318 ms) +galaxy.jobs.handler INFO 2024-10-05 07:00:23,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:23,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 141 +galaxy.jobs DEBUG 2024-10-05 07:00:23,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [141] prepared (73.458 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:00:23,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/141/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/141/registry.xml' '/galaxy/server/database/jobs_directory/000/141/upload_params.json' '190:/galaxy/server/database/objects/e/5/7/dataset_e5711e30-b370-4ca7-b0a0-cf50ca64030b_files:/galaxy/server/database/objects/e/5/7/dataset_e5711e30-b370-4ca7-b0a0-cf50ca64030b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:00:23,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (141) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/141/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/141/galaxy_141.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:23,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 141 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:23,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 141 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:23,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:33,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-27948 with k8s id: gxy-27948 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:00:34,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 140: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:34,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9624z with k8s id: gxy-9624z succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:00:35,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 141: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:00:43,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 140 finished +galaxy.model.metadata DEBUG 2024-10-05 07:00:43,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 189 +galaxy.jobs INFO 2024-10-05 07:00:43,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 140 in /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs DEBUG 2024-10-05 07:00:43,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 140 executed (106.399 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:43,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 140 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 07:00:44,682 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 141 finished +galaxy.model.metadata DEBUG 2024-10-05 07:00:44,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 190 +galaxy.jobs INFO 2024-10-05 07:00:44,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 141 in /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs DEBUG 2024-10-05 07:00:44,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 141 executed (94.140 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:44,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 141 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:00:45,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 142 +tpv.core.entities DEBUG 2024-10-05 07:00:45,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:00:45,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:00:45,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:00:45,624 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:00:45,651 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Working directory for job is: /galaxy/server/database/jobs_directory/000/142 +galaxy.jobs.runners DEBUG 2024-10-05 07:00:45,661 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [142] queued (49.299 ms) +galaxy.jobs.handler INFO 2024-10-05 07:00:45,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:45,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 142 +galaxy.jobs DEBUG 2024-10-05 07:00:45,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [142] prepared (57.778 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:00:45,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:00:45,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1: chromeister:1.5.a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:00:45,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/chromeister:1.5.a--h031d066_5,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:00:45,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/142/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/2/9/0/dataset_29085765-63a5-45ce-af65-700da8961e1b.dat 'mycoplasma-232.fasta' && ln -s /galaxy/server/database/objects/e/5/7/dataset_e5711e30-b370-4ca7-b0a0-cf50ca64030b.dat 'mycoplasma-7422.fasta' && CHROMEISTER -query 'mycoplasma-232.fasta' -db 'mycoplasma-7422.fasta' -dimension 1000 -kmer 16 -diffuse 3 -out 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat && compute_score-nogrid.R 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat 1000 > '/galaxy/server/database/objects/b/e/d/dataset_bed2ae46-c29e-489a-bda4-78a6024d95a9.dat' && detect_events.py 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.raw.txt png && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.png '/galaxy/server/database/objects/e/5/a/dataset_e5a3b465-352e-442f-bfbd-b45319ac8dbd.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat '/galaxy/server/database/objects/8/e/3/dataset_8e38f460-ef91-437f-81bb-6e48055db2aa.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.filt.png '/galaxy/server/database/objects/8/7/7/dataset_87746d12-fb3a-4697-8a32-15b255e28b38.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.txt '/galaxy/server/database/objects/e/a/e/dataset_eae87982-91a0-44a2-8282-aec6d17e0bb7.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.csv '/galaxy/server/database/objects/3/9/d/dataset_39deb19c-8550-4bda-b429-cb30d2bfbf54.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:00:45,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (142) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/142/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/142/galaxy_142.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:45,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 142 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:00:45,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:00:45,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1: chromeister:1.5.a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:00:45,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/chromeister:1.5.a--h031d066_5,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:45,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 142 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:00:46,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:25,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-jjs5f with k8s id: gxy-jjs5f succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:01:25,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 142: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:01:34,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 142 finished +galaxy.model.metadata DEBUG 2024-10-05 07:01:34,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 191 +galaxy.model.metadata DEBUG 2024-10-05 07:01:34,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 192 +galaxy.model.metadata DEBUG 2024-10-05 07:01:34,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 193 +galaxy.model.metadata DEBUG 2024-10-05 07:01:34,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 194 +galaxy.model.metadata DEBUG 2024-10-05 07:01:34,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 195 +galaxy.model.metadata DEBUG 2024-10-05 07:01:34,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 196 +galaxy.util WARNING 2024-10-05 07:01:34,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/e/3/dataset_8e38f460-ef91-437f-81bb-6e48055db2aa.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/e/3/dataset_8e38f460-ef91-437f-81bb-6e48055db2aa.dat' +galaxy.util WARNING 2024-10-05 07:01:34,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/8/7/7/dataset_87746d12-fb3a-4697-8a32-15b255e28b38.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/8/7/7/dataset_87746d12-fb3a-4697-8a32-15b255e28b38.dat' +galaxy.util WARNING 2024-10-05 07:01:34,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/9/d/dataset_39deb19c-8550-4bda-b429-cb30d2bfbf54.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/9/d/dataset_39deb19c-8550-4bda-b429-cb30d2bfbf54.dat' +galaxy.util WARNING 2024-10-05 07:01:34,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/a/e/dataset_eae87982-91a0-44a2-8282-aec6d17e0bb7.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/a/e/dataset_eae87982-91a0-44a2-8282-aec6d17e0bb7.dat' +galaxy.util WARNING 2024-10-05 07:01:34,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/5/a/dataset_e5a3b465-352e-442f-bfbd-b45319ac8dbd.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/5/a/dataset_e5a3b465-352e-442f-bfbd-b45319ac8dbd.dat' +galaxy.jobs INFO 2024-10-05 07:01:34,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 142 in /galaxy/server/database/jobs_directory/000/142 +galaxy.jobs DEBUG 2024-10-05 07:01:34,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 142 executed (161.276 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:34,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 142 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:01:37,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 143 +tpv.core.entities DEBUG 2024-10-05 07:01:37,736 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:01:37,737 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:01:37,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:01:37,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:01:37,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Working directory for job is: /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs.runners DEBUG 2024-10-05 07:01:37,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [143] queued (33.852 ms) +galaxy.jobs.handler INFO 2024-10-05 07:01:37,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:37,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 143 +galaxy.jobs DEBUG 2024-10-05 07:01:37,860 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [143] prepared (73.336 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:01:37,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/143/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/143/registry.xml' '/galaxy/server/database/jobs_directory/000/143/upload_params.json' '197:/galaxy/server/database/objects/0/4/a/dataset_04a950dd-498a-4982-9433-feb9c35e042d_files:/galaxy/server/database/objects/0/4/a/dataset_04a950dd-498a-4982-9433-feb9c35e042d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:01:37,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (143) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/143/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/143/galaxy_143.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:37,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 143 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:37,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 143 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:38,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-10-05 07:01:38,782 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 144 +tpv.core.entities DEBUG 2024-10-05 07:01:38,810 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:01:38,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:01:38,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:01:38,831 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:01:38,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Working directory for job is: /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs.runners DEBUG 2024-10-05 07:01:38,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [144] queued (38.362 ms) +galaxy.jobs.handler INFO 2024-10-05 07:01:38,857 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:38,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 144 +galaxy.jobs DEBUG 2024-10-05 07:01:38,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [144] prepared (73.242 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:01:38,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/144/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/144/registry.xml' '/galaxy/server/database/jobs_directory/000/144/upload_params.json' '198:/galaxy/server/database/objects/2/4/6/dataset_246e1e63-0184-4aa2-8898-822fb50bd206_files:/galaxy/server/database/objects/2/4/6/dataset_246e1e63-0184-4aa2-8898-822fb50bd206.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:01:38,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (144) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/144/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/144/galaxy_144.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:38,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:38,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:39,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-r8mkj with k8s id: gxy-r8mkj succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-27wfq failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-27wfq. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,847 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 07:01:49,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-27wfq + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-27wfq": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (144/gxy-27wfq) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (144/gxy-27wfq) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (144/gxy-27wfq) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (144/gxy-27wfq) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-27wfq. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Attempting to stop job 144 (gxy-27wfq) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Found job with id gxy-27wfq to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 07:01:49,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 143: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:49,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (144/gxy-27wfq) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-10-05 07:01:59,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 143 finished +galaxy.model.metadata DEBUG 2024-10-05 07:01:59,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 197 +galaxy.jobs INFO 2024-10-05 07:01:59,112 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 143 in /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs DEBUG 2024-10-05 07:01:59,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 143 executed (100.243 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:01:59,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 143 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:02:00,279 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 145 +tpv.core.entities DEBUG 2024-10-05 07:02:00,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:02:00,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:02:00,313 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:02:00,325 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:02:00,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Working directory for job is: /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs.runners DEBUG 2024-10-05 07:02:00,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [145] queued (32.857 ms) +galaxy.jobs.handler INFO 2024-10-05 07:02:00,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:00,350 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 145 +galaxy.jobs DEBUG 2024-10-05 07:02:00,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [145] prepared (99.028 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:02:00,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/145/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/145/registry.xml' '/galaxy/server/database/jobs_directory/000/145/upload_params.json' '199:/galaxy/server/database/objects/f/c/5/dataset_fc52f6db-4dd1-4b05-a701-0c03b3aef759_files:/galaxy/server/database/objects/f/c/5/dataset_fc52f6db-4dd1-4b05-a701-0c03b3aef759.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:02:00,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (145) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/145/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/145/galaxy_145.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:00,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 145 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:00,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 145 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:02:01,352 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 146 +tpv.core.entities DEBUG 2024-10-05 07:02:01,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:02:01,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:02:01,389 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:02:01,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:02:01,421 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Working directory for job is: /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs.runners DEBUG 2024-10-05 07:02:01,428 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [146] queued (39.412 ms) +galaxy.jobs.handler INFO 2024-10-05 07:02:01,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:01,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 146 +galaxy.jobs DEBUG 2024-10-05 07:02:01,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [146] prepared (80.111 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:02:01,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/146/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/146/registry.xml' '/galaxy/server/database/jobs_directory/000/146/upload_params.json' '200:/galaxy/server/database/objects/6/8/b/dataset_68b24101-70a7-4a47-bd9f-a6877d17388d_files:/galaxy/server/database/objects/6/8/b/dataset_68b24101-70a7-4a47-bd9f-a6877d17388d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:02:01,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (146) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/146/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/146/galaxy_146.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:01,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 146 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:01,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 146 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:01,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:01,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:12,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-bbqnj with k8s id: gxy-bbqnj succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:02:12,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 145: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:13,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9wvk9 with k8s id: gxy-9wvk9 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:02:13,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 146: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:02:22,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 145 finished +galaxy.model.metadata DEBUG 2024-10-05 07:02:22,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 199 +galaxy.jobs INFO 2024-10-05 07:02:22,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 145 in /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs DEBUG 2024-10-05 07:02:22,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 145 executed (105.083 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:22,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 145 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 07:02:22,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 146 finished +galaxy.model.metadata DEBUG 2024-10-05 07:02:23,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 200 +galaxy.jobs INFO 2024-10-05 07:02:23,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 146 in /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs DEBUG 2024-10-05 07:02:23,090 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 146 executed (89.895 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:23,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 146 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:02:24,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 147 +tpv.core.entities DEBUG 2024-10-05 07:02:24,163 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:02:24,163 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:02:24,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:02:24,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:02:24,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Working directory for job is: /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs.runners DEBUG 2024-10-05 07:02:24,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [147] queued (44.525 ms) +galaxy.jobs.handler INFO 2024-10-05 07:02:24,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:24,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 147 +galaxy.jobs DEBUG 2024-10-05 07:02:24,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [147] prepared (62.104 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:02:24,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:02:24,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1: chromeister:1.5.a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:02:24,313 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/chromeister:1.5.a--h031d066_5,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:02:24,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/147/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/f/c/5/dataset_fc52f6db-4dd1-4b05-a701-0c03b3aef759.dat 'mycoplasma-232.fasta' && ln -s /galaxy/server/database/objects/6/8/b/dataset_68b24101-70a7-4a47-bd9f-a6877d17388d.dat 'mycoplasma-7422.fasta' && CHROMEISTER -query 'mycoplasma-232.fasta' -db 'mycoplasma-7422.fasta' -dimension 1000 -kmer 32 -diffuse 4 -out 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat && compute_score-nogrid.R 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat 1000 > '/galaxy/server/database/objects/7/d/2/dataset_7d283864-923c-4790-a6f6-c45520ab1efc.dat' && detect_events.py 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.raw.txt png && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.png '/galaxy/server/database/objects/f/e/7/dataset_fe77d406-3e94-426f-992c-1291a345685d.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat '/galaxy/server/database/objects/6/0/c/dataset_60c59b16-0be7-46f0-a378-d3519a9cf604.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.filt.png '/galaxy/server/database/objects/c/7/9/dataset_c79b0f12-e56e-4585-8adc-15c30fe5ca5b.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.txt '/galaxy/server/database/objects/a/d/2/dataset_ad21fc79-a73f-40ce-b827-8809c2c3da7e.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.csv '/galaxy/server/database/objects/0/5/7/dataset_057bcd25-4cf7-42df-97ff-565fb29ba395.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:02:24,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (147) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/147/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/147/galaxy_147.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:24,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 147 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:02:24,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:02:24,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1: chromeister:1.5.a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:02:24,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/chromeister:1.5.a--h031d066_5,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:24,423 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 147 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:02:25,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:03,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xwbzk with k8s id: gxy-xwbzk succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:03:04,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 147: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:03:13,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 147 finished +galaxy.model.metadata DEBUG 2024-10-05 07:03:13,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 201 +galaxy.model.metadata DEBUG 2024-10-05 07:03:13,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 202 +galaxy.model.metadata DEBUG 2024-10-05 07:03:13,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 203 +galaxy.model.metadata DEBUG 2024-10-05 07:03:13,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 204 +galaxy.model.metadata DEBUG 2024-10-05 07:03:13,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 205 +galaxy.model.metadata DEBUG 2024-10-05 07:03:13,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 206 +galaxy.util WARNING 2024-10-05 07:03:13,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/0/c/dataset_60c59b16-0be7-46f0-a378-d3519a9cf604.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/0/c/dataset_60c59b16-0be7-46f0-a378-d3519a9cf604.dat' +galaxy.util WARNING 2024-10-05 07:03:13,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/7/9/dataset_c79b0f12-e56e-4585-8adc-15c30fe5ca5b.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/7/9/dataset_c79b0f12-e56e-4585-8adc-15c30fe5ca5b.dat' +galaxy.util WARNING 2024-10-05 07:03:13,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/0/5/7/dataset_057bcd25-4cf7-42df-97ff-565fb29ba395.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/0/5/7/dataset_057bcd25-4cf7-42df-97ff-565fb29ba395.dat' +galaxy.util WARNING 2024-10-05 07:03:13,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/d/2/dataset_ad21fc79-a73f-40ce-b827-8809c2c3da7e.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/d/2/dataset_ad21fc79-a73f-40ce-b827-8809c2c3da7e.dat' +galaxy.util WARNING 2024-10-05 07:03:13,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/e/7/dataset_fe77d406-3e94-426f-992c-1291a345685d.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/e/7/dataset_fe77d406-3e94-426f-992c-1291a345685d.dat' +galaxy.jobs INFO 2024-10-05 07:03:13,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 147 in /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs DEBUG 2024-10-05 07:03:13,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 147 executed (158.777 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:13,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 147 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:03:21,327 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 148 +tpv.core.entities DEBUG 2024-10-05 07:03:21,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:03:21,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:03:21,359 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:03:21,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:03:21,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Working directory for job is: /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs.runners DEBUG 2024-10-05 07:03:21,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [148] queued (34.715 ms) +galaxy.jobs.handler INFO 2024-10-05 07:03:21,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:21,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 148 +galaxy.jobs DEBUG 2024-10-05 07:03:21,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [148] prepared (77.596 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:03:21,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/148/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/148/registry.xml' '/galaxy/server/database/jobs_directory/000/148/upload_params.json' '207:/galaxy/server/database/objects/a/5/1/dataset_a51e1e99-de95-4116-8713-abffc74aa5f4_files:/galaxy/server/database/objects/a/5/1/dataset_a51e1e99-de95-4116-8713-abffc74aa5f4.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:03:21,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (148) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/148/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/148/galaxy_148.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:21,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 148 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:21,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 148 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:21,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:32,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2gdl9 with k8s id: gxy-2gdl9 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:03:32,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 148: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:03:41,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 148 finished +galaxy.model.metadata DEBUG 2024-10-05 07:03:41,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 207 +galaxy.jobs INFO 2024-10-05 07:03:41,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 148 in /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs DEBUG 2024-10-05 07:03:41,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 148 executed (92.754 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:41,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 148 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:03:41,782 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 149 +tpv.core.entities DEBUG 2024-10-05 07:03:41,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/.*, abstract=False, cores=1, mem=15.2, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:03:41,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:03:41,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:03:41,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:03:41,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Working directory for job is: /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs.runners DEBUG 2024-10-05 07:03:41,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [149] queued (32.510 ms) +galaxy.jobs.handler INFO 2024-10-05 07:03:41,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:41,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 149 +galaxy.jobs DEBUG 2024-10-05 07:03:41,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [149] prepared (52.010 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:03:41,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:03:41,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:03:42,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:03:42,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/149/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/149/outputs/COMMAND_VERSION 2>&1; +lofreq filter -i /galaxy/server/database/objects/a/5/1/dataset_a51e1e99-de95-4116-8713-abffc74aa5f4.dat --no-defaults --verbose -Q 38 -K 20 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf] +galaxy.jobs.runners DEBUG 2024-10-05 07:03:42,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (149) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/149/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/149/galaxy_149.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/149/working/filtered.vcf" -a -f "/galaxy/server/database/objects/e/7/9/dataset_e7923a75-91d5-4ece-b83e-de2131874541.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/149/working/filtered.vcf" "/galaxy/server/database/objects/e/7/9/dataset_e7923a75-91d5-4ece-b83e-de2131874541.dat" ; fi; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:42,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 149 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:03:42,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:03:42,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:03:42,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:42,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 149 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:43,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:03:51,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-nx64m with k8s id: gxy-nx64m succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:03:51,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 149: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:04:00,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 149 finished +galaxy.model.metadata DEBUG 2024-10-05 07:04:00,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 208 +galaxy.util WARNING 2024-10-05 07:04:00,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/7/9/dataset_e7923a75-91d5-4ece-b83e-de2131874541.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/7/9/dataset_e7923a75-91d5-4ece-b83e-de2131874541.dat' +galaxy.jobs INFO 2024-10-05 07:04:00,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 149 in /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs DEBUG 2024-10-05 07:04:00,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 149 executed (112.985 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:00,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 149 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:04:02,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 150 +tpv.core.entities DEBUG 2024-10-05 07:04:02,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:04:02,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:04:02,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:04:02,306 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:04:02,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Working directory for job is: /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs.runners DEBUG 2024-10-05 07:04:02,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [150] queued (36.064 ms) +galaxy.jobs.handler INFO 2024-10-05 07:04:02,332 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:02,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 150 +galaxy.jobs DEBUG 2024-10-05 07:04:02,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [150] prepared (83.307 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:04:02,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/150/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/150/registry.xml' '/galaxy/server/database/jobs_directory/000/150/upload_params.json' '209:/galaxy/server/database/objects/6/1/b/dataset_61b191bf-4c4b-4111-94a4-54ea72aa853d_files:/galaxy/server/database/objects/6/1/b/dataset_61b191bf-4c4b-4111-94a4-54ea72aa853d.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:04:02,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (150) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/150/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/150/galaxy_150.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:02,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 150 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:02,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 150 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:03,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:13,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rtq9g with k8s id: gxy-rtq9g succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:04:13,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 150: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:04:22,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 150 finished +galaxy.model.metadata DEBUG 2024-10-05 07:04:22,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 209 +galaxy.jobs INFO 2024-10-05 07:04:22,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 150 in /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs DEBUG 2024-10-05 07:04:22,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 150 executed (112.624 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:22,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 150 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:04:23,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 151 +tpv.core.entities DEBUG 2024-10-05 07:04:23,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/.*, abstract=False, cores=1, mem=15.2, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:04:23,777 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:04:23,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:04:23,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:04:23,806 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Working directory for job is: /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs.runners DEBUG 2024-10-05 07:04:23,815 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [151] queued (33.833 ms) +galaxy.jobs.handler INFO 2024-10-05 07:04:23,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:23,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 151 +galaxy.jobs DEBUG 2024-10-05 07:04:23,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [151] prepared (42.417 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:23,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:04:23,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:24,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:04:24,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/151/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/151/outputs/COMMAND_VERSION 2>&1; +lofreq filter -i /galaxy/server/database/objects/6/1/b/dataset_61b191bf-4c4b-4111-94a4-54ea72aa853d.dat --no-defaults --verbose --only-snvs -q bonf -r 0.01 -s 66 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf] +galaxy.jobs.runners DEBUG 2024-10-05 07:04:24,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (151) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/151/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/151/galaxy_151.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/151/working/filtered.vcf" -a -f "/galaxy/server/database/objects/1/d/9/dataset_1d944da3-6d04-4098-8713-bc0ca516d61f.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/151/working/filtered.vcf" "/galaxy/server/database/objects/1/d/9/dataset_1d944da3-6d04-4098-8713-bc0ca516d61f.dat" ; fi; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:24,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:24,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:04:24,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:24,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:24,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:24,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-z4vrp failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-z4vrp. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 07:04:28,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-z4vrp + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-z4vrp": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (151/gxy-z4vrp) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (151/gxy-z4vrp) tool_stderr: Skipping default settings +At least one type of multiple testing correction requested. Doing first pass of vcf +MTC application completed +Successful exit. + +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (151/gxy-z4vrp) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (151/gxy-z4vrp) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-z4vrp. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 151 (gxy-z4vrp) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-z4vrp to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:28,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (151/gxy-z4vrp) Terminated at user's request +galaxy.util WARNING 2024-10-05 07:04:28,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/d/9/dataset_1d944da3-6d04-4098-8713-bc0ca516d61f.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/d/9/dataset_1d944da3-6d04-4098-8713-bc0ca516d61f.dat' +galaxy.jobs.handler DEBUG 2024-10-05 07:04:29,917 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 152 +tpv.core.entities DEBUG 2024-10-05 07:04:29,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:04:29,946 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:04:29,949 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:04:29,960 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:04:29,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Working directory for job is: /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs.runners DEBUG 2024-10-05 07:04:29,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [152] queued (32.043 ms) +galaxy.jobs.handler INFO 2024-10-05 07:04:29,984 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:29,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 152 +galaxy.jobs DEBUG 2024-10-05 07:04:30,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [152] prepared (73.711 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:04:30,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/152/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/152/registry.xml' '/galaxy/server/database/jobs_directory/000/152/upload_params.json' '211:/galaxy/server/database/objects/9/7/d/dataset_97d63900-5460-4902-b167-15f48e99dfad_files:/galaxy/server/database/objects/9/7/d/dataset_97d63900-5460-4902-b167-15f48e99dfad.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:04:30,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (152) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/152/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/152/galaxy_152.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:30,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 152 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:30,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 152 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:30,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:40,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-shk8t with k8s id: gxy-shk8t succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:04:40,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 152: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:04:49,780 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 152 finished +galaxy.model.metadata DEBUG 2024-10-05 07:04:49,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 211 +galaxy.jobs INFO 2024-10-05 07:04:49,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 152 in /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs DEBUG 2024-10-05 07:04:49,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 152 executed (89.700 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:49,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 152 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:04:50,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 153 +tpv.core.entities DEBUG 2024-10-05 07:04:50,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/.*, abstract=False, cores=1, mem=15.2, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:04:50,443 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:04:50,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:04:50,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:04:50,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Working directory for job is: /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs.runners DEBUG 2024-10-05 07:04:50,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [153] queued (51.822 ms) +galaxy.jobs.handler INFO 2024-10-05 07:04:50,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:50,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 153 +galaxy.jobs DEBUG 2024-10-05 07:04:50,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [153] prepared (67.316 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:50,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:04:50,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:50,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:04:50,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/153/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/153/outputs/COMMAND_VERSION 2>&1; +lofreq filter -i /galaxy/server/database/objects/9/7/d/dataset_97d63900-5460-4902-b167-15f48e99dfad.dat --no-defaults --verbose --print-all -Q 38 -K 20 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf] +galaxy.jobs.runners DEBUG 2024-10-05 07:04:50,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (153) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/153/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/153/galaxy_153.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/153/working/filtered.vcf" -a -f "/galaxy/server/database/objects/4/0/b/dataset_40bfe36e-c463-4fc2-a3bf-2864562aef2a.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/153/working/filtered.vcf" "/galaxy/server/database/objects/4/0/b/dataset_40bfe36e-c463-4fc2-a3bf-2864562aef2a.dat" ; fi; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:50,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 153 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:50,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:04:50,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:04:50,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:50,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 153 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:50,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:04:54,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-bjg25 with k8s id: gxy-bjg25 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:04:55,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 153: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:05:04,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 153 finished +galaxy.model.metadata DEBUG 2024-10-05 07:05:04,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 212 +galaxy.util WARNING 2024-10-05 07:05:04,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/0/b/dataset_40bfe36e-c463-4fc2-a3bf-2864562aef2a.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/0/b/dataset_40bfe36e-c463-4fc2-a3bf-2864562aef2a.dat' +galaxy.jobs INFO 2024-10-05 07:05:04,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 153 in /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs DEBUG 2024-10-05 07:05:04,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 153 executed (98.466 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:04,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 153 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:05:06,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 154 +tpv.core.entities DEBUG 2024-10-05 07:05:06,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:05:06,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:05:06,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:05:06,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:05:06,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Working directory for job is: /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs.runners DEBUG 2024-10-05 07:05:06,877 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [154] queued (34.239 ms) +galaxy.jobs.handler INFO 2024-10-05 07:05:06,880 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:06,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 154 +galaxy.jobs DEBUG 2024-10-05 07:05:06,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [154] prepared (77.867 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:05:06,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/154/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/154/registry.xml' '/galaxy/server/database/jobs_directory/000/154/upload_params.json' '213:/galaxy/server/database/objects/1/d/4/dataset_1d4f8abd-efaa-4624-bd3c-b3f60566401b_files:/galaxy/server/database/objects/1/d/4/dataset_1d4f8abd-efaa-4624-bd3c-b3f60566401b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:05:06,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (154) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/154/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/154/galaxy_154.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:07,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:07,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:08,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:18,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-86gcv with k8s id: gxy-86gcv succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:05:18,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 154: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:05:27,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 154 finished +galaxy.model.metadata DEBUG 2024-10-05 07:05:27,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 213 +galaxy.jobs INFO 2024-10-05 07:05:27,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 154 in /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs DEBUG 2024-10-05 07:05:27,474 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 154 executed (93.496 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:27,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:05:28,298 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 155 +tpv.core.entities DEBUG 2024-10-05 07:05:28,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:05:28,331 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:05:28,335 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:05:28,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:05:28,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Working directory for job is: /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs.runners DEBUG 2024-10-05 07:05:28,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [155] queued (38.586 ms) +galaxy.jobs.handler INFO 2024-10-05 07:05:28,376 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:28,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 155 +galaxy.jobs DEBUG 2024-10-05 07:05:28,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [155] prepared (52.562 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:05:28,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:05:28,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:05:28,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:05:28,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/155/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/155/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/d/4/dataset_1d4f8abd-efaa-4624-bd3c-b3f60566401b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools query --list-samples input.vcf.gz | tee /galaxy/server/database/objects/5/5/3/dataset_553d831b-e819-43fe-ae15-b7bcfb4121b7.dat | tr '\n' ','] +galaxy.jobs.runners DEBUG 2024-10-05 07:05:28,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (155) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/155/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/155/galaxy_155.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:28,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 155 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:05:28,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:05:28,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:05:28,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:28,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 155 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:29,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:39,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ghbtw with k8s id: gxy-ghbtw succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:05:39,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 155: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:05:48,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 155 finished +galaxy.model.metadata DEBUG 2024-10-05 07:05:48,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 214 +galaxy.jobs INFO 2024-10-05 07:05:48,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 155 in /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs DEBUG 2024-10-05 07:05:48,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 155 executed (98.530 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:48,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 155 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:05:50,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 157, 156 +tpv.core.entities DEBUG 2024-10-05 07:05:50,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:05:50,840 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:05:50,844 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:05:50,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:05:50,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Working directory for job is: /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs.runners DEBUG 2024-10-05 07:05:50,877 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [156] queued (32.992 ms) +galaxy.jobs.handler INFO 2024-10-05 07:05:50,879 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:50,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 156 +tpv.core.entities DEBUG 2024-10-05 07:05:50,890 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:05:50,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:05:50,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:05:50,907 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:05:50,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Working directory for job is: /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs.runners DEBUG 2024-10-05 07:05:50,942 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [157] queued (47.165 ms) +galaxy.jobs.handler INFO 2024-10-05 07:05:50,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:50,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 157 +galaxy.jobs DEBUG 2024-10-05 07:05:50,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [156] prepared (98.986 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:05:51,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/156/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/156/registry.xml' '/galaxy/server/database/jobs_directory/000/156/upload_params.json' '215:/galaxy/server/database/objects/b/6/6/dataset_b66abd4d-5959-48c5-b442-99aab280fd23_files:/galaxy/server/database/objects/b/6/6/dataset_b66abd4d-5959-48c5-b442-99aab280fd23.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:05:51,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (156) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/156/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/156/galaxy_156.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 07:05:51,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [157] prepared (80.020 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:51,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:51,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 07:05:51,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/157/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/157/registry.xml' '/galaxy/server/database/jobs_directory/000/157/upload_params.json' '216:/galaxy/server/database/objects/9/9/d/dataset_99d340be-9e6c-4d18-884e-f983f109d93b_files:/galaxy/server/database/objects/9/9/d/dataset_99d340be-9e6c-4d18-884e-f983f109d93b.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:05:51,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (157) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/157/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/157/galaxy_157.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:51,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 157 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:51,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 157 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:51,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:05:51,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-mbb25 failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-mbb25. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 07:06:01,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-mbb25 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-mbb25": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-m8l6f with k8s id: gxy-m8l6f succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (156/gxy-mbb25) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (156/gxy-mbb25) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (156/gxy-mbb25) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (156/gxy-mbb25) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-mbb25. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Attempting to stop job 156 (gxy-mbb25) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Found job with id gxy-mbb25 to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:01,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:02,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (156/gxy-mbb25) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-10-05 07:06:02,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 157: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.handler DEBUG 2024-10-05 07:06:03,177 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 159, 158 +tpv.core.entities DEBUG 2024-10-05 07:06:03,206 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:06:03,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:06:03,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:06:03,223 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:06:03,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Working directory for job is: /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs.runners DEBUG 2024-10-05 07:06:03,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [158] queued (33.507 ms) +galaxy.jobs.handler INFO 2024-10-05 07:06:03,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:03,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 158 +tpv.core.entities DEBUG 2024-10-05 07:06:03,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:06:03,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:06:03,264 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:06:03,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:06:03,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Working directory for job is: /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs.runners DEBUG 2024-10-05 07:06:03,314 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [159] queued (49.085 ms) +galaxy.jobs.handler INFO 2024-10-05 07:06:03,319 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:03,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 159 +galaxy.jobs DEBUG 2024-10-05 07:06:03,356 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [158] prepared (94.645 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:06:03,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/158/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/158/registry.xml' '/galaxy/server/database/jobs_directory/000/158/upload_params.json' '217:/galaxy/server/database/objects/5/d/5/dataset_5d593d25-a18d-4bc4-8879-415e4c93a208_files:/galaxy/server/database/objects/5/d/5/dataset_5d593d25-a18d-4bc4-8879-415e4c93a208.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:06:03,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (158) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/158/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/158/galaxy_158.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 07:06:03,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [159] prepared (84.359 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:03,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 158 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 07:06:03,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/159/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/159/registry.xml' '/galaxy/server/database/jobs_directory/000/159/upload_params.json' '218:/galaxy/server/database/objects/7/1/1/dataset_7110b5ee-99a6-4a08-9242-21d4949e81ab_files:/galaxy/server/database/objects/7/1/1/dataset_7110b5ee-99a6-4a08-9242-21d4949e81ab.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:06:03,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (159) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/159/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/159/galaxy_159.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:03,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 159 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:03,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 158 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:03,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 159 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:04,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:04,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners DEBUG 2024-10-05 07:06:11,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 157 finished +galaxy.model.metadata DEBUG 2024-10-05 07:06:11,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 216 +galaxy.jobs INFO 2024-10-05 07:06:11,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 157 in /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs DEBUG 2024-10-05 07:06:11,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 157 executed (98.689 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:11,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 157 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:15,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-psmh6 with k8s id: gxy-psmh6 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:15,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tfv5q with k8s id: gxy-tfv5q succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:06:15,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 158: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:06:15,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 159: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:06:24,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 158 finished +galaxy.jobs.runners DEBUG 2024-10-05 07:06:24,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 159 finished +galaxy.model.metadata DEBUG 2024-10-05 07:06:25,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 217 +galaxy.model.metadata DEBUG 2024-10-05 07:06:25,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 218 +galaxy.jobs INFO 2024-10-05 07:06:25,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 159 in /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs INFO 2024-10-05 07:06:25,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 158 in /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs DEBUG 2024-10-05 07:06:25,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 159 executed (138.730 ms) +galaxy.jobs DEBUG 2024-10-05 07:06:25,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 158 executed (147.527 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:25,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 159 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:25,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 158 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:06:26,067 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 160 +tpv.core.entities DEBUG 2024-10-05 07:06:26,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:06:26,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:06:26,109 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:06:26,122 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:06:26,136 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Working directory for job is: /galaxy/server/database/jobs_directory/000/160 +galaxy.jobs.runners DEBUG 2024-10-05 07:06:26,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [160] queued (36.361 ms) +galaxy.jobs.handler INFO 2024-10-05 07:06:26,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (160) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:26,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 160 +galaxy.jobs DEBUG 2024-10-05 07:06:26,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [160] prepared (79.123 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:06:26,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:06:26,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:06:26,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:06:26,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/160/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/160/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/d/5/dataset_5d593d25-a18d-4bc4-8879-415e4c93a208.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/7/1/1/dataset_7110b5ee-99a6-4a08-9242-21d4949e81ab.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools isec --nfiles "=2" --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/1/7/6/dataset_1765ae0b-dd64-4352-abe0-88e7d22846ad.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:06:26,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (160) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/160/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/160/galaxy_160.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:26,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 160 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:06:26,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:06:26,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-10-05 07:06:26,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:26,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 160 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:27,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:31,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xb4h8 with k8s id: gxy-xb4h8 succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:06:31,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 160: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:06:40,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 160 finished +galaxy.model.metadata DEBUG 2024-10-05 07:06:40,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 219 +galaxy.jobs INFO 2024-10-05 07:06:40,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 160 in /galaxy/server/database/jobs_directory/000/160 +galaxy.jobs DEBUG 2024-10-05 07:06:40,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 160 executed (98.413 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:40,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 160 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:06:43,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 162, 161 +tpv.core.entities DEBUG 2024-10-05 07:06:43,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:06:43,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:06:43,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:06:43,572 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:06:43,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Working directory for job is: /galaxy/server/database/jobs_directory/000/161 +galaxy.jobs.runners DEBUG 2024-10-05 07:06:43,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [161] queued (32.569 ms) +galaxy.jobs.handler INFO 2024-10-05 07:06:43,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (161) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:43,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 161 +tpv.core.entities DEBUG 2024-10-05 07:06:43,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:06:43,607 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:06:43,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:06:43,624 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:06:43,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Working directory for job is: /galaxy/server/database/jobs_directory/000/162 +galaxy.jobs.runners DEBUG 2024-10-05 07:06:43,661 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [162] queued (49.391 ms) +galaxy.jobs.handler INFO 2024-10-05 07:06:43,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (162) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:43,667 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 162 +galaxy.jobs DEBUG 2024-10-05 07:06:43,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [161] prepared (87.724 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:06:43,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/161/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/161/registry.xml' '/galaxy/server/database/jobs_directory/000/161/upload_params.json' '220:/galaxy/server/database/objects/0/c/2/dataset_0c2059cc-0f54-488d-8266-34305b8c22e5_files:/galaxy/server/database/objects/0/c/2/dataset_0c2059cc-0f54-488d-8266-34305b8c22e5.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:06:43,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (161) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/161/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/161/galaxy_161.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-10-05 07:06:43,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [162] prepared (77.639 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:06:43,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/162/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/162/registry.xml' '/galaxy/server/database/jobs_directory/000/162/upload_params.json' '221:/galaxy/server/database/objects/2/a/a/dataset_2aa68304-0db2-4d2c-9959-176a7d6ae6cf_files:/galaxy/server/database/objects/2/a/a/dataset_2aa68304-0db2-4d2c-9959-176a7d6ae6cf.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:43,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 161 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-10-05 07:06:43,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (162) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/162/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/162/galaxy_162.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:43,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 162 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:43,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 161 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:43,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 162 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:44,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:44,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-nxf4z failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-nxf4z. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 161 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-10-05 07:06:54,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-10-05-06-10-1/jobs/gxy-nxf4z + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-nxf4z": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-lkbn8 with k8s id: gxy-lkbn8 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161/gxy-nxf4z) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161/gxy-nxf4z) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161/gxy-nxf4z) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161/gxy-nxf4z) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-nxf4z. +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 161 (gxy-nxf4z) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-nxf4z to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:54,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 161 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:55,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (161/gxy-nxf4z) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-10-05 07:06:55,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 162: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.handler DEBUG 2024-10-05 07:06:56,917 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 163 +tpv.core.entities DEBUG 2024-10-05 07:06:56,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:06:56,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:06:56,951 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:06:56,963 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:06:56,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Working directory for job is: /galaxy/server/database/jobs_directory/000/163 +galaxy.jobs.runners DEBUG 2024-10-05 07:06:56,984 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [163] queued (33.107 ms) +galaxy.jobs.handler INFO 2024-10-05 07:06:56,987 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (163) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:56,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 163 +galaxy.jobs DEBUG 2024-10-05 07:06:57,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [163] prepared (83.123 ms) +galaxy.jobs.command_factory INFO 2024-10-05 07:06:57,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/163/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/163/registry.xml' '/galaxy/server/database/jobs_directory/000/163/upload_params.json' '222:/galaxy/server/database/objects/1/2/e/dataset_12ee58c3-4bb8-454d-9d2c-18783fff2c6c_files:/galaxy/server/database/objects/1/2/e/dataset_12ee58c3-4bb8-454d-9d2c-18783fff2c6c.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:06:57,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (163) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/163/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/163/galaxy_163.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:57,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 163 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:57,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 163 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:06:57,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners DEBUG 2024-10-05 07:07:04,169 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 162 finished +galaxy.model.metadata DEBUG 2024-10-05 07:07:04,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 221 +galaxy.jobs INFO 2024-10-05 07:07:04,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 162 in /galaxy/server/database/jobs_directory/000/162 +galaxy.jobs DEBUG 2024-10-05 07:07:04,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 162 executed (85.094 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:04,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 162 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:08,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-58kxd with k8s id: gxy-58kxd succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:07:08,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 163: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:07:17,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 163 finished +galaxy.model.metadata DEBUG 2024-10-05 07:07:17,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 222 +galaxy.jobs INFO 2024-10-05 07:07:17,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 163 in /galaxy/server/database/jobs_directory/000/163 +galaxy.jobs DEBUG 2024-10-05 07:07:17,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 163 executed (95.400 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:17,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 163 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:07:18,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 164 +tpv.core.entities DEBUG 2024-10-05 07:07:18,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:07:18,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:07:18,455 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:07:18,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:07:18,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Working directory for job is: /galaxy/server/database/jobs_directory/000/164 +galaxy.jobs.runners DEBUG 2024-10-05 07:07:18,488 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [164] queued (32.557 ms) +galaxy.jobs.handler INFO 2024-10-05 07:07:18,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (164) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:18,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 164 +galaxy.jobs DEBUG 2024-10-05 07:07:18,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [164] prepared (43.327 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:07:18,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:07:18,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:07:18,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:07:18,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/164/tool_script.sh] for tool command [vcfrandomsample -p 1 -r 0.2 '/galaxy/server/database/objects/1/2/e/dataset_12ee58c3-4bb8-454d-9d2c-18783fff2c6c.dat' > '/galaxy/server/database/objects/3/1/b/dataset_31b88afb-a64c-4f2d-8f32-35225db5c755.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:07:18,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (164) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/164/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/164/galaxy_164.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:18,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 164 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:07:18,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:07:18,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:07:18,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:18,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 164 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:19,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:29,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vfhfj with k8s id: gxy-vfhfj succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:07:29,423 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 164: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:07:38,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 164 finished +galaxy.model.metadata DEBUG 2024-10-05 07:07:38,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 223 +galaxy.jobs INFO 2024-10-05 07:07:38,560 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 164 in /galaxy/server/database/jobs_directory/000/164 +galaxy.jobs DEBUG 2024-10-05 07:07:38,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 164 executed (89.560 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:38,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 164 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:07:41,058 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 165, 167, 166 +tpv.core.entities DEBUG 2024-10-05 07:07:41,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:07:41,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:07:41,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:07:41,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:07:41,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Working directory for job is: /galaxy/server/database/jobs_directory/000/165 +galaxy.jobs.runners DEBUG 2024-10-05 07:07:41,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [165] queued (33.701 ms) +galaxy.jobs.handler INFO 2024-10-05 07:07:41,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (165) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 165 +tpv.core.entities DEBUG 2024-10-05 07:07:41,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:07:41,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:07:41,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:07:41,160 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:07:41,184 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Working directory for job is: /galaxy/server/database/jobs_directory/000/166 +galaxy.jobs.runners DEBUG 2024-10-05 07:07:41,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [166] queued (47.868 ms) +galaxy.jobs.handler INFO 2024-10-05 07:07:41,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (166) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 166 +tpv.core.entities DEBUG 2024-10-05 07:07:41,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:07:41,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:07:41,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:07:41,237 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:07:41,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [165] prepared (96.784 ms) +galaxy.jobs DEBUG 2024-10-05 07:07:41,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Working directory for job is: /galaxy/server/database/jobs_directory/000/167 +galaxy.jobs.command_factory INFO 2024-10-05 07:07:41,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/165/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/165/registry.xml' '/galaxy/server/database/jobs_directory/000/165/upload_params.json' '224:/galaxy/server/database/objects/3/f/8/dataset_3f8f3e4c-859a-42c9-ad05-b3495f625800_files:/galaxy/server/database/objects/3/f/8/dataset_3f8f3e4c-859a-42c9-ad05-b3495f625800.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:07:41,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [167] queued (56.880 ms) +galaxy.jobs.handler INFO 2024-10-05 07:07:41,278 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (167) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 167 +galaxy.jobs.runners DEBUG 2024-10-05 07:07:41,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (165) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/165/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/165/galaxy_165.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 165 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 07:07:41,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [166] prepared (105.487 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 165 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 07:07:41,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/166/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/166/registry.xml' '/galaxy/server/database/jobs_directory/000/166/upload_params.json' '225:/galaxy/server/database/objects/d/0/3/dataset_d031afb9-109c-4f5f-9a2b-ec8adce2d710_files:/galaxy/server/database/objects/d/0/3/dataset_d031afb9-109c-4f5f-9a2b-ec8adce2d710.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:07:41,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (166) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/166/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/166/galaxy_166.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 166 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 07:07:41,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [167] prepared (92.233 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,391 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 166 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-10-05 07:07:41,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/167/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/167/registry.xml' '/galaxy/server/database/jobs_directory/000/167/upload_params.json' '226:/galaxy/server/database/objects/3/a/1/dataset_3a19bd15-8f50-4631-b1e3-a393cf69da60_files:/galaxy/server/database/objects/3/a/1/dataset_3a19bd15-8f50-4631-b1e3-a393cf69da60.dat'] +galaxy.jobs.runners DEBUG 2024-10-05 07:07:41,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (167) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/167/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/167/galaxy_167.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 167 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:41,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 167 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:42,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:42,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:42,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:52,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rg2mn with k8s id: gxy-rg2mn succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:52,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5tqlp with k8s id: gxy-5tqlp succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:07:52,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-jbtsm with k8s id: gxy-jbtsm succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:07:53,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 165: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:07:53,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 166: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:07:53,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 167: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:08:07,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 166 finished +galaxy.jobs.runners DEBUG 2024-10-05 07:08:07,200 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 165 finished +galaxy.jobs.runners DEBUG 2024-10-05 07:08:07,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 167 finished +galaxy.model.metadata DEBUG 2024-10-05 07:08:07,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 225 +galaxy.model.metadata DEBUG 2024-10-05 07:08:07,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 224 +galaxy.jobs INFO 2024-10-05 07:08:07,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 166 in /galaxy/server/database/jobs_directory/000/166 +galaxy.model.metadata DEBUG 2024-10-05 07:08:07,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 226 +galaxy.jobs INFO 2024-10-05 07:08:07,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 165 in /galaxy/server/database/jobs_directory/000/165 +galaxy.jobs INFO 2024-10-05 07:08:07,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 167 in /galaxy/server/database/jobs_directory/000/167 +galaxy.jobs DEBUG 2024-10-05 07:08:07,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 166 executed (158.417 ms) +galaxy.jobs DEBUG 2024-10-05 07:08:07,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 165 executed (163.805 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:07,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 166 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:07,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 165 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-10-05 07:08:07,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 167 executed (133.610 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:07,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 167 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-10-05 07:08:08,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 168 +tpv.core.entities DEBUG 2024-10-05 07:08:08,112 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'tpv_cores': '{cores}', 'tpv_gpus': '{gpus}', 'tpv_mem': '{mem}', 'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=0, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-10-05 07:08:08,112 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-10-05 07:08:08,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-10-05 07:08:08,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-10-05 07:08:08,144 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Working directory for job is: /galaxy/server/database/jobs_directory/000/168 +galaxy.jobs.runners DEBUG 2024-10-05 07:08:08,153 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [168] queued (36.604 ms) +galaxy.jobs.handler INFO 2024-10-05 07:08:08,156 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (168) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:08,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 168 +galaxy.jobs DEBUG 2024-10-05 07:08:08,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [168] prepared (49.755 ms) +galaxy.tool_util.deps.containers INFO 2024-10-05 07:08:08,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:08:08,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0: mulled-v2-98ddb1f3cf1349cc3c286418d2895004e1791819:fae61fa977b1364550a2df32f067b432629eced7 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:08:08,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-98ddb1f3cf1349cc3c286418d2895004e1791819:fae61fa977b1364550a2df32f067b432629eced7-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-10-05 07:08:08,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/168/tool_script.sh] for tool command [ivar version | grep version > /galaxy/server/database/jobs_directory/000/168/outputs/COMMAND_VERSION 2>&1; +ivar getmasked -i '/galaxy/server/database/objects/3/f/8/dataset_3f8f3e4c-859a-42c9-ad05-b3495f625800.dat' -b '/galaxy/server/database/objects/d/0/3/dataset_d031afb9-109c-4f5f-9a2b-ec8adce2d710.dat' -f '/galaxy/server/database/objects/3/a/1/dataset_3a19bd15-8f50-4631-b1e3-a393cf69da60.dat' -p masked_primers] +galaxy.jobs.runners DEBUG 2024-10-05 07:08:08,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (168) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/168/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/168/galaxy_168.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/168/working/masked_primers.txt" -a -f "/galaxy/server/database/objects/6/4/4/dataset_644ee5b5-b73b-4b4c-8cca-a061f89f13a6.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/168/working/masked_primers.txt" "/galaxy/server/database/objects/6/4/4/dataset_644ee5b5-b73b-4b4c-8cca-a061f89f13a6.dat" ; fi; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:08,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 168 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-10-05 07:08:08,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-10-05 07:08:08,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0: mulled-v2-98ddb1f3cf1349cc3c286418d2895004e1791819:fae61fa977b1364550a2df32f067b432629eced7 +galaxy.tool_util.deps.containers INFO 2024-10-05 07:08:08,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-98ddb1f3cf1349cc3c286418d2895004e1791819:fae61fa977b1364550a2df32f067b432629eced7-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:08,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 168 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:09,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:16,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zb9nd with k8s id: gxy-zb9nd succeeded +galaxy.jobs.runners DEBUG 2024-10-05 07:08:16,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 168: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-10-05 07:08:25,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 168 finished +galaxy.model.metadata DEBUG 2024-10-05 07:08:25,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 227 +galaxy.util WARNING 2024-10-05 07:08:25,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/4/4/dataset_644ee5b5-b73b-4b4c-8cca-a061f89f13a6.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/4/4/dataset_644ee5b5-b73b-4b4c-8cca-a061f89f13a6.dat' +galaxy.jobs INFO 2024-10-05 07:08:25,189 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 168 in /galaxy/server/database/jobs_directory/000/168 +galaxy.jobs DEBUG 2024-10-05 07:08:25,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 168 executed (95.556 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-10-05 07:08:25,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 168 is an interactive tool. guest ports: []. interactive entry points: [] diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/jobs.txt b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/jobs.txt new file mode 100644 index 000000000..f4012147c --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/jobs.txt @@ -0,0 +1,168 @@ +c10d58b0c4a4c37d ok 2024-10-05T07:08:25.191774 toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0 +9cea879b0cd34941 ok 2024-10-05T07:08:07.364009 upload1 +01b6ad12a51a0610 ok 2024-10-05T07:08:07.330260 upload1 +c16c5464adfef9b8 ok 2024-10-05T07:08:07.323074 upload1 +2d27de61c475e487 ok 2024-10-05T07:07:38.562664 toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0 +e8cd6d5fd3b3b82f ok 2024-10-05T07:07:17.517770 upload1 +88ff02288943c7b4 ok 2024-10-05T07:07:04.244318 upload1 +b3289f59ef3f0719 error 2024-10-05T07:06:55.045087 upload1 +6d0793221f983d04 ok 2024-10-05T07:06:40.935628 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4 +43bb98568f0d76d9 ok 2024-10-05T07:06:25.098869 upload1 +26e494e06d7aa357 ok 2024-10-05T07:06:25.090316 upload1 +ab010cea83aef04a ok 2024-10-05T07:06:11.331467 upload1 +faa5496b14d1cee0 error 2024-10-05T07:06:02.066043 upload1 +b6200d2975339489 ok 2024-10-05T07:05:48.667283 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4 +a98703bac41e5fd0 ok 2024-10-05T07:05:27.442177 upload1 +fda5aebbce7c2848 ok 2024-10-05T07:05:04.202765 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 +75bd376bb51bf5cf ok 2024-10-05T07:04:49.856337 upload1 +a4f48caaf7d6de64 error 2024-10-05T07:04:28.694841 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 +9ddf4d6c37c686e2 ok 2024-10-05T07:04:22.691935 upload1 +91958e131477903f ok 2024-10-05T07:04:00.333743 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 +39a9f26a41b0fa22 ok 2024-10-05T07:03:41.348033 upload1 +aeb10c489f7558cc ok 2024-10-05T07:03:13.425402 toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1 +9f84c7897e4a143f ok 2024-10-05T07:02:23.053798 upload1 +0f9c4b64c088aaa5 ok 2024-10-05T07:02:22.208702 upload1 +6694697af5dcbdcd ok 2024-10-05T07:01:59.115362 upload1 +8b790c9bf7dcddba error 2024-10-05T07:01:49.985880 upload1 +0e0dc0e56adbe5f4 ok 2024-10-05T07:01:34.885098 toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1 +bd65503ad7a9af55 ok 2024-10-05T07:00:44.765079 upload1 +87645111b5c153cf ok 2024-10-05T07:00:43.665034 upload1 +6b6250d123b0f899 ok 2024-10-05T07:00:19.090214 toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1 +d2a0fb0371b60f8b ok 2024-10-05T06:59:09.966058 upload1 +602ebc097ebb9c60 ok 2024-10-05T06:59:09.160841 upload1 +6e41773d9f6e8bd7 ok 2024-10-05T06:58:45.320096 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +0e9e51d5e353c5ed ok 2024-10-05T06:58:29.803691 upload1 +9bda54e87fae793b ok 2024-10-05T06:58:29.769070 upload1 +31a28c5e839cb4d7 ok 2024-10-05T06:58:06.775705 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +ff764b8b794f379f ok 2024-10-05T06:57:52.440600 upload1 +9bb35db4a4a6eb79 ok 2024-10-05T06:57:52.157383 upload1 +26af5c92b2c39c3f ok 2024-10-05T06:57:28.278239 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +eece88bfac2c788c ok 2024-10-05T06:57:12.437907 upload1 +f638c659a1b65910 ok 2024-10-05T06:57:12.425994 upload1 +3f44ab3096ffcc1e ok 2024-10-05T06:56:48.499833 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +5f4d96ea980a6855 ok 2024-10-05T06:56:30.746817 upload1 +c1e4e0ab9c464d65 ok 2024-10-05T06:56:28.725833 upload1 +fa49e059f52f6619 ok 2024-10-05T06:56:06.097432 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +db1e84f0148fb5d2 ok 2024-10-05T06:55:50.923797 upload1 +b0417aefeb5a24d9 ok 2024-10-05T06:55:28.809117 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +535cbca629a5b5c5 ok 2024-10-05T06:55:13.620045 upload1 +c3da5b6d7e1b446e ok 2024-10-05T06:54:51.343750 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +9f979cc9eed714b5 ok 2024-10-05T06:54:37.405129 upload1 +f43133f4c6d4bc45 error 2024-10-05T06:54:14.906118 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +859c2327b2fb1bbb ok 2024-10-05T06:54:09.562025 upload1 +3bdef6d60132b40e error 2024-10-05T06:53:47.319910 upload1 +6940f01d49f3eab7 ok 2024-10-05T06:53:34.247049 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +4f43e4bab50ab9e8 ok 2024-10-05T06:53:16.181762 upload1 +ab25a5964fc57582 ok 2024-10-05T06:52:51.897921 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +4b7e4165841ed691 ok 2024-10-05T06:52:37.266100 upload1 +40224001529b2140 ok 2024-10-05T06:52:37.176798 upload1 +ce25846ce630107d ok 2024-10-05T06:52:13.151509 upload1 +0fdf1ba82854cc66 ok 2024-10-05T06:51:51.076502 upload1 +87ef64afd1491f87 ok 2024-10-05T06:51:27.799765 upload1 +5117f9fea7c22917 ok 2024-10-05T06:51:04.733981 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +89258c891e92939f ok 2024-10-05T06:50:49.086001 upload1 +d80facd9fa7307a4 ok 2024-10-05T06:50:48.976130 upload1 +898527f9e130834e ok 2024-10-05T06:50:25.146255 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +0a03cf8dcdf43b0d ok 2024-10-05T06:50:09.234837 upload1 +af11950b36af14f2 ok 2024-10-05T06:50:08.354287 upload1 +67075bd0b9719099 ok 2024-10-05T06:49:45.469841 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +6e285b05558ea69e ok 2024-10-05T06:49:30.515615 upload1 +7762f557498ed15a ok 2024-10-05T06:49:29.667808 upload1 +9584a994c964fa4e ok 2024-10-05T06:49:05.135667 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +b4fe30a1a633f5de ok 2024-10-05T06:48:50.206981 upload1 +f76bfe820ed3b20b ok 2024-10-05T06:48:49.565693 upload1 +c5fc2b4acde50290 ok 2024-10-05T06:48:26.466020 upload1 +5bd5320b2e464c49 ok 2024-10-05T06:48:04.280043 upload1 +bc41f3629c2908b8 ok 2024-10-05T06:47:43.080875 upload1 +1fea2b9adc2a0fce ok 2024-10-05T06:47:19.038693 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +1901d0f883d04f28 ok 2024-10-05T06:47:03.258107 upload1 +37c06a92dc334c3a ok 2024-10-05T06:47:03.211491 upload1 +20a79f958a1ad4a1 ok 2024-10-05T06:46:40.186772 upload1 +db5a2d4573973b22 error 2024-10-05T06:46:29.872394 upload1 +75502bcd39344a71 ok 2024-10-05T06:46:16.576095 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2 +a542d32b05dfe07d ok 2024-10-05T06:45:57.123454 upload1 +06e787421fe23b00 ok 2024-10-05T06:45:56.904116 upload1 +066e0eaa4712a55e error 2024-10-05T06:45:32.749018 toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0 +b31fdeb32a759538 ok 2024-10-05T06:45:26.163975 upload1 +e15b5fabc0e0db09 ok 2024-10-05T06:45:02.575710 toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0 +95d74e7f0ce53721 ok 2024-10-05T06:44:22.423032 upload1 +ba22c5388737214c ok 2024-10-05T06:43:56.881047 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +322ba939561d06a2 ok 2024-10-05T06:43:41.841210 upload1 +923aa3d77495e5ac ok 2024-10-05T06:43:41.796852 upload1 +31b2e24d62e0696c ok 2024-10-05T06:43:40.602420 upload1 +717ae31659bceb0b ok 2024-10-05T06:43:13.086294 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +29d16f7835a3b20c ok 2024-10-05T06:42:57.462316 upload1 +e9ee55cd2e7bf4a6 ok 2024-10-05T06:42:56.382581 upload1 +cc3b53475dde1ae6 ok 2024-10-05T06:42:33.337686 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +3987271c9954af00 ok 2024-10-05T06:42:19.152174 upload1 +255807e99aba0cae ok 2024-10-05T06:42:19.044553 upload1 +1ded0489bef80358 ok 2024-10-05T06:42:18.044017 upload1 +5018ff1d4058493c ok 2024-10-05T06:41:51.400325 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +d2f410c19987bd26 ok 2024-10-05T06:41:36.084999 upload1 +025396b06fd9f207 ok 2024-10-05T06:41:36.063825 upload1 +ee358a7876520820 ok 2024-10-05T06:41:34.808668 upload1 +4ce93ab10a6e1c73 ok 2024-10-05T06:41:07.474473 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18 +1f12ff881de39bf8 ok 2024-10-05T06:40:47.791276 upload1 +b87b31416b004e12 ok 2024-10-05T06:40:47.711939 upload1 +2704ccb375827a9b error 2024-10-05T06:40:23.333336 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +943a976c3b379a43 ok 2024-10-05T06:40:16.939101 upload1 +e8de2f61a615df46 ok 2024-10-05T06:40:15.924675 upload1 +53f38b9dd2170918 ok 2024-10-05T06:39:53.041171 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +7693fd1fe15f87a1 ok 2024-10-05T06:39:35.854474 upload1 +f75ceb0d2a04a38b ok 2024-10-05T06:39:35.776697 upload1 +a4ef26c5b1d85e43 ok 2024-10-05T06:39:35.694314 upload1 +fdadf5367d57b093 error 2024-10-05T06:39:08.059295 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +2d7776aa9c65c125 ok 2024-10-05T06:39:00.922309 upload1 +d07edbc21b354e8b ok 2024-10-05T06:38:59.947025 upload1 +f4138b5273f88dd0 ok 2024-10-05T06:38:59.784515 upload1 +d5536ca3b8f0f513 ok 2024-10-05T06:38:31.519298 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +68409fbd9c58c51a ok 2024-10-05T06:38:14.849258 upload1 +3832b9e5941b7549 ok 2024-10-05T06:38:14.809079 upload1 +4480654f925b6a3c ok 2024-10-05T06:37:50.838531 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +09d0be24709df7c6 ok 2024-10-05T06:37:33.340670 upload1 +8d5ba2a42a846f1e ok 2024-10-05T06:37:33.226002 upload1 +1fee1f4d1ec01669 ok 2024-10-05T06:37:09.413817 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +5522a3a41dfc9140 ok 2024-10-05T06:36:53.225396 upload1 +52ebb49230a9336d ok 2024-10-05T06:36:29.974148 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +e4b55125ba5df844 ok 2024-10-05T06:36:13.451223 upload1 +34502251f8acb6a5 ok 2024-10-05T06:36:13.387121 upload1 +1b92f046e5cab3f6 ok 2024-10-05T06:35:50.577591 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +d87d0e2fffaa3f70 ok 2024-10-05T06:35:33.239218 upload1 +e72e27a949e65cd5 ok 2024-10-05T06:35:32.372634 upload1 +644229f8e32129db ok 2024-10-05T06:35:32.337366 upload1 +e3b889d4657a05fb ok 2024-10-05T06:35:03.768090 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +76653ab899b01292 ok 2024-10-05T06:34:47.063612 upload1 +f65c28f8078c8e36 ok 2024-10-05T06:34:46.936060 upload1 +e65491e2306bc743 ok 2024-10-05T06:34:45.869554 upload1 +a0fd35a64b34d145 ok 2024-10-05T06:34:18.987909 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +9c4145df767100b6 ok 2024-10-05T06:34:02.091818 upload1 +2a1b1d1392ee3f4b ok 2024-10-05T06:34:02.037094 upload1 +8f69013b205acde1 ok 2024-10-05T06:33:38.367236 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +51fab3a282c1b839 ok 2024-10-05T06:33:22.664037 upload1 +a8ac4943e45d3e9e ok 2024-10-05T06:33:21.725725 upload1 +e74073ea01a7986a ok 2024-10-05T06:32:58.960915 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +46c7a3aa42d6d50e ok 2024-10-05T06:32:42.059328 upload1 +3cdb8d8f0a4afc83 ok 2024-10-05T06:32:17.485947 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +a93ae86c4d410a1d ok 2024-10-05T06:32:00.410136 upload1 +c423ba2a54f14448 ok 2024-10-05T06:32:00.286678 upload1 +94c43bfedefe7dde ok 2024-10-05T06:31:49.301326 upload1 +f15263fcf651e071 ok 2024-10-05T06:31:48.409583 upload1 +d9efec2f13a62343 error 2024-10-05T06:31:38.502256 upload1 +29ee25cbd61b509a ok 2024-10-05T06:31:25.225150 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +5ec7144545af8589 ok 2024-10-05T06:31:09.011288 upload1 +13fc19f852e156cc ok 2024-10-05T06:31:08.994522 upload1 +abdc18f794870e73 ok 2024-10-05T06:31:08.803610 upload1 +894592df6446a85c ok 2024-10-05T06:30:40.050542 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +564fc2db207e950b ok 2024-10-05T06:30:22.587562 upload1 +567bf1b8a805ea99 ok 2024-10-05T06:30:22.577994 upload1 +b0b52e3f9cc1f16b ok 2024-10-05T06:29:58.710262 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +39af4bea4dd23079 ok 2024-10-05T06:29:41.870550 upload1 +955d69d7bee06518 ok 2024-10-05T06:29:40.893765 upload1 +a152032facdcc291 ok 2024-10-05T06:29:19.267794 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 +fde2515219921d15 ok 2024-10-05T06:28:48.597981 upload1 +fb91bae129b08fde ok 2024-10-05T06:28:25.369842 upload1 +39a53760c56001e8 error 2024-10-05T06:28:15.264725 upload1 +57809ef5376e1992 error 2024-10-05T06:28:01.140320 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0 +1e4681385ecc7453 ok 2024-10-05T06:27:29.260875 upload1 +3b88da29b42d9d34 ok 2024-10-05T06:26:56.007295 toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1 +779d4cab783f0ad5 ok 2024-10-05T06:26:15.138982 upload1 diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/node-info.txt b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/node-info.txt new file mode 100644 index 000000000..c7b5b6be0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/node-info.txt @@ -0,0 +1,147 @@ +Name: gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 +Roles: +Labels: beta.kubernetes.io/arch=amd64 + beta.kubernetes.io/instance-type=e2-custom-20-81920 + beta.kubernetes.io/os=linux + cloud.google.com/gke-boot-disk=pd-balanced + cloud.google.com/gke-container-runtime=containerd + cloud.google.com/gke-cpu-scaling-level=20 + cloud.google.com/gke-logging-variant=DEFAULT + cloud.google.com/gke-max-pods-per-node=110 + cloud.google.com/gke-memory-gb-scaling-level=81 + cloud.google.com/gke-nodepool=default-pool + cloud.google.com/gke-os-distribution=cos + cloud.google.com/gke-provisioning=standard + cloud.google.com/gke-stack-type=IPV4 + cloud.google.com/machine-family=e2 + cloud.google.com/private-node=false + failure-domain.beta.kubernetes.io/region=us-east1 + failure-domain.beta.kubernetes.io/zone=us-east1-b + kubernetes.io/arch=amd64 + kubernetes.io/hostname=gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 + kubernetes.io/os=linux + node.kubernetes.io/instance-type=e2-custom-20-81920 + topology.gke.io/zone=us-east1-b + topology.kubernetes.io/region=us-east1 + topology.kubernetes.io/zone=us-east1-b +Annotations: container.googleapis.com/instance_id: 1538987721298372145 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5","pd.csi.storage.gke.io":"projects/anvil-and-terra-development/zo... + node.alpha.kubernetes.io/ttl: 0 + node.gke.io/last-applied-node-labels: + cloud.google.com/gke-boot-disk=pd-balanced,cloud.google.com/gke-container-runtime=containerd,cloud.google.com/gke-cpu-scaling-level=20,clo... + node.gke.io/last-applied-node-taints: + volumes.kubernetes.io/controller-managed-attach-detach: true +CreationTimestamp: Sat, 05 Oct 2024 06:17:09 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 + AcquireTime: + RenewTime: Sat, 05 Oct 2024 07:08:59 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + FrequentContainerdRestart False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 NoFrequentContainerdRestart containerd is functioning properly + DeprecatedUsingV1Alpha2Cri False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 DeprecatedUsingV1Alpha2CriNotDetected No deprecation risk: did not use v1alpha2 CRI + DeprecatedOtherContainerdFeatures False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 DeprecatedOtherContainerdFeaturesNotDetected No deprecation risk: did not find any deprecations other than 3 configs fields (auths/configs/mirrors), pulling schema v1 images and using v1alpha2 CRI. + SysctlChanged False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 SysctlNotChanged Default sysctls are in effect, no unexpected sysctl changes + CorruptDockerOverlay2 False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + FrequentDockerRestart False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 NoFrequentDockerRestart docker is functioning properly + DeprecatedMirrorsFieldInContainerdConfiguration False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 DeprecatedMirrorsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'mirrors' field in containerd's config + ReadonlyFilesystem False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + FrequentUnregisterNetDevice False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 NoFrequentUnregisterNetDevice node is functioning properly + KernelDeadlock False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 KernelHasNoDeadlock kernel has no deadlock + FrequentKubeletRestart False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 NoFrequentKubeletRestart kubelet is functioning properly + DeprecatedConfigsFieldInContainerdConfiguration False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 DeprecatedConfigsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'configs' field in containerd's config + DeprecatedPullingSchemaV1Image False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 DeprecatedPullingSchemaV1ImageDetected No deprecation risk: did not pull any schema v1 images + DeprecatedAuthsFieldInContainerdConfiguration False Sat, 05 Oct 2024 07:07:17 +0000 Sat, 05 Oct 2024 06:17:11 +0000 DeprecatedAuthsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'auths' field in containerd's config + NetworkUnavailable False Sat, 05 Oct 2024 06:17:10 +0000 Sat, 05 Oct 2024 06:17:09 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Sat, 05 Oct 2024 07:07:48 +0000 Sat, 05 Oct 2024 06:16:40 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Sat, 05 Oct 2024 07:07:48 +0000 Sat, 05 Oct 2024 06:16:40 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Sat, 05 Oct 2024 07:07:48 +0000 Sat, 05 Oct 2024 06:16:40 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Sat, 05 Oct 2024 07:07:48 +0000 Sat, 05 Oct 2024 06:17:29 +0000 KubeletReady kubelet is posting ready status +Addresses: + InternalIP: 10.142.0.49 + ExternalIP: 35.243.180.33 +Capacity: + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82368040Ki + pods: 110 +Allocatable: + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75553320Ki + pods: 110 +System Info: + Machine ID: 2d52b8296204e822c16f7951ef28fd6f + System UUID: 2d52b829-6204-e822-c16f-7951ef28fd6f + Boot ID: 0fd451b7-1ef4-428c-9826-2c33cf7516fb + Kernel Version: 6.1.100+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.7.19 + Kubelet Version: v1.30.3-gke.1969002 + Kube-Proxy Version: v1.30.3-gke.1969002 +PodCIDR: 10.80.0.0/24 +PodCIDRs: 10.80.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 +Non-terminated Pods: (27 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-cvmfscsi-controllerplugin-8487f78556m5khw 0 (0%) 0 (0%) 0 (0%) 0 (0%) 49m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-cvmfscsi-nodeplugin-l2zwm 0 (0%) 0 (0%) 0 (0%) 0 (0%) 45m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-celery-6c9b88cd9d-t9p5n 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-celery-beat-6f8d88f759-kpxmz 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-job-0-69d57bf4f7-wwznx 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-nginx-858c74965b-54wtf 100m (0%) 2 (10%) 500M (0%) 3G (3%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-web-58f59bf98f-xmrbb 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-galaxy-workflow-5dcb544d8c-hpscw 500m (2%) 2 (10%) 2G (2%) 8G (10%) 48m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 49m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-rabbitmq-59566d6659-8rfqx 100m (0%) 150m (0%) 128Mi (0%) 192Mi (0%) 49m + edge-24-10-05-06-10-1 edge-24-10-05-06-10-1-rabbitmq-messaging-topology-operator98blp 100m (0%) 150m (0%) 128Mi (0%) 192Mi (0%) 49m + gke-managed-cim kube-state-metrics-0 105m (0%) 0 (0%) 130Mi (0%) 530Mi (0%) 52m + gmp-system collector-5wjkd 5m (0%) 0 (0%) 36M (0%) 3032M (3%) 51m + gmp-system gmp-operator-55c55d9dc7-qvv58 1m (0%) 0 (0%) 16M (0%) 2G (2%) 52m + kube-system event-exporter-gke-78fb679b7b-qfvwn 3m (0%) 0 (0%) 100Mi (0%) 0 (0%) 52m + kube-system fluentbit-gke-zxg6w 105m (0%) 1 (5%) 230Mi (0%) 530Mi (0%) 51m + kube-system gke-metrics-agent-5ljn2 19m (0%) 1 (5%) 155Mi (0%) 155Mi (0%) 51m + kube-system konnectivity-agent-5dfc8c76f5-kmll2 15m (0%) 0 (0%) 60Mi (0%) 155Mi (0%) 52m + kube-system konnectivity-agent-autoscaler-897d4f648-qn2qt 10m (0%) 0 (0%) 10M (0%) 0 (0%) 52m + kube-system kube-dns-58ffdb4bb6-qp252 265m (1%) 0 (0%) 140Mi (0%) 240Mi (0%) 52m + kube-system kube-dns-autoscaler-6f896b6968-rdjdp 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 52m + kube-system kube-proxy-gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 100m (0%) 0 (0%) 0 (0%) 0 (0%) 50m + kube-system l7-default-backend-6697bb6dfd-4rqs5 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 52m + kube-system metrics-server-v1.30.3-54cbdc6d8-lhbzg 43m (0%) 43m (0%) 55Mi (0%) 55Mi (0%) 52m + kube-system pdcsi-node-f2whd 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 51m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4761m (23%) 16343m (82%) + memory 14211044480 (18%) 52432873472 (67%) + ephemeral-storage 35940Mi (80%) 204Gi (465%) + hugepages-1Gi 0 (0%) 0 (0%) + hugepages-2Mi 0 (0%) 0 (0%) +Events: + Type Reason Age From Message + ---- ------ ---- ---- ------- + Normal Starting 51m kube-proxy + Normal Starting 55m kubelet Starting kubelet. + Warning InvalidDiskCapacity 55m kubelet invalid capacity 0 on image filesystem + Normal NodeAllocatableEnforced 55m kubelet Updated Node Allocatable limit across pods + Normal NodeHasNoDiskPressure 53m (x7 over 55m) kubelet Node gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 53m (x7 over 55m) kubelet Node gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 53m (x8 over 55m) kubelet Node gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 status is now: NodeHasSufficientMemory + Normal Synced 51m cloud-node-controller Node synced successfully + Warning NodeRegistrationCheckerStart 51m node-registration-checker-monitor Sat Oct 5 06:13:13 UTC 2024 - ** Starting Node Registration Checker ** + Normal RegisteredNode 51m node-controller Node gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 event: Registered Node gke-edge-24-10-05-06-10-default-pool-26ba7d06-dcd5 in Controller + Warning NodeRegistrationCheckerDidNotRunChecks 48m node-registration-checker-monitor Sat Oct 5 06:20:14 UTC 2024 - ** Node ready and registered. ** diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html new file mode 100644 index 000000000..ad02fe2a0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.json b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.json new file mode 100644 index 000000000..ffd082363 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 73, "errors": 19, "failures": 6, "skips": 2}, "tests": [{"id": "bcftools_isec/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_isec", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 12.10615587234497, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_isec/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_isec", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 38.97197604179382, "inputs": {"input_files": [{"src": "hda", "id": "b74a0420a86f2454"}, {"src": "hda", "id": "450bb44b79c28759"}], "sec_restrict|regions_overlap": "1", "sec_default|nfiles": "=2", "output_type": "v"}, "job": {"model_class": "Job", "id": "6d0793221f983d04", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:06:25.307548", "update_time": "2024-10-05T07:06:40.935628", "galaxy_version": "24.1", "external_id": "gxy-xb4h8", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/d/5/dataset_5d593d25-a18d-4bc4-8879-415e4c93a208.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/7/1/1/dataset_7110b5ee-99a6-4a08-9242-21d4949e81ab.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools isec --nfiles \"=2\" --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/1/7/6/dataset_1765ae0b-dd64-4352-abe0-88e7d22846ad.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"complement\": false, \"nfiles\": \"=2\"}", "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_files": {"id": "b74a0420a86f2454", "src": "hda", "uuid": "5d593d25-a18d-4bc4-8879-415e4c93a208"}, "input_files1": {"id": "b74a0420a86f2454", "src": "hda", "uuid": "5d593d25-a18d-4bc4-8879-415e4c93a208"}, "input_files2": {"id": "450bb44b79c28759", "src": "hda", "uuid": "7110b5ee-99a6-4a08-9242-21d4949e81ab"}}, "outputs": {"output_file": {"id": "a6c6e7d92ca4ef03", "src": "hda", "uuid": "1765ae0b-dd64-4352-abe0-88e7d22846ad"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: -w option not given, printing list of sites...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: -w option not given, printing list of sites...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-10-05 07:06:28", "plugin": "core", "name": "end_epoch", "raw_value": "1728111988.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 07:06:27", "plugin": "core", "name": "start_epoch", "raw_value": "1728111987.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_query_list_samples/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_query_list_samples", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 43.63984036445618, "inputs": {"input_file": {"src": "hda", "id": "d01ff4e63c41d2db"}}, "job": {"model_class": "Job", "id": "b6200d2975339489", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:05:27.647363", "update_time": "2024-10-05T07:05:48.667283", "galaxy_version": "24.1", "external_id": "gxy-ghbtw", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/d/4/dataset_1d4f8abd-efaa-4624-bd3c-b3f60566401b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools query --list-samples input.vcf.gz | tee /galaxy/server/database/objects/5/5/3/dataset_553d831b-e819-43fe-ae15-b7bcfb4121b7.dat | tr '\\n' ','", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_file": {"id": "d01ff4e63c41d2db", "src": "hda", "uuid": "1d4f8abd-efaa-4624-bd3c-b3f60566401b"}}, "outputs": {"output_file": {"id": "7ae11f7e89a58dd4", "src": "hda", "uuid": "553d831b-e819-43fe-ae15-b7bcfb4121b7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "C,D,", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "C,D,", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-10-05 07:05:34", "plugin": "core", "name": "end_epoch", "raw_value": "1728111934.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 07:05:33", "plugin": "core", "name": "start_epoch", "raw_value": "1728111933.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-0", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 0, "time_seconds": 43.01922845840454, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "37c06a92dc334c3a"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "1fea2b9adc2a0fce"}, "input_type|input_type_selector": "single", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "4ce93ab10a6e1c73", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:40:48.079580", "update_time": "2024-10-05T06:41:07.474473", "galaxy_version": "24.1", "external_id": "gxy-j8cwt", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/8/3/7/dataset_837dc26e-1024-4181-bc1a-658376dde6c4.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat' > first.sai && bwa samse 'localref.fa' first.sai '/galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/1/b/e/dataset_1be8f42d-946d-4a6f-92dd-40dfb355dba4.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 2, \"adv_se_options\": {\"__current_case__\": 1, \"adv_se_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 92, \"src\": \"hda\"}]}, \"input_type_selector\": \"single\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 91, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "37c06a92dc334c3a", "src": "hda", "uuid": "837dc26e-1024-4181-bc1a-658376dde6c4"}, "input_type|fastq_input1": {"id": "1fea2b9adc2a0fce", "src": "hda", "uuid": "67b63bff-02ed-4e68-96df-056661a1451e"}}, "outputs": {"bam_output": {"id": "bc41f3629c2908b8", "src": "hda", "uuid": "1be8f42d-946d-4a6f-92dd-40dfb355dba4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.044 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat\n[main] Real time: 0.015 sec; CPU: 0.043 sec\n[bwa_aln_core] convert to sequence coordinate... 0.00 sec\n[bwa_aln_core] refine gapped alignments... 0.00 sec\n[bwa_aln_core] print alignments... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa samse localref.fa first.sai /galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat\n[main] Real time: 0.006 sec; CPU: 0.003 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.044 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat\n[main] Real time: 0.015 sec; CPU: 0.043 sec\n[bwa_aln_core] convert to sequence coordinate... 0.00 sec\n[bwa_aln_core] refine gapped alignments... 0.00 sec\n[bwa_aln_core] print alignments... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa samse localref.fa first.sai /galaxy/server/database/objects/6/7/b/dataset_67b63bff-02ed-4e68-96df-056661a1451e.dat\n[main] Real time: 0.006 sec; CPU: 0.003 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:40:53", "plugin": "core", "name": "end_epoch", "raw_value": "1728110453.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:40:53", "plugin": "core", "name": "start_epoch", "raw_value": "1728110453.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-1", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 1, "time_seconds": 44.03389549255371, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "5bd5320b2e464c49"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "c5fc2b4acde50290"}, "input_type|fastq_input2": {"src": "hda", "id": "b4fe30a1a633f5de"}, "input_type|input_type_selector": "paired", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "5018ff1d4058493c", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:41:36.244995", "update_time": "2024-10-05T06:41:51.400325", "galaxy_version": "24.1", "external_id": "gxy-wl6c8", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/5/2/d/dataset_52db4d9d-1352-4a9a-be6d-b2863b0d2e98.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat' '/galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/1/b/8/dataset_1b8ef26f-453c-4fc7-bbd3-64c914cfd768.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 0, \"adv_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 96, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "5bd5320b2e464c49", "src": "hda", "uuid": "52db4d9d-1352-4a9a-be6d-b2863b0d2e98"}, "input_type|fastq_input1": {"id": "c5fc2b4acde50290", "src": "hda", "uuid": "74e2fea9-fbb1-4152-82e0-669a6e59e45c"}, "input_type|fastq_input2": {"id": "b4fe30a1a633f5de", "src": "hda", "uuid": "24214749-c6a2-4963-95fa-4aa89b880b53"}}, "outputs": {"bam_output": {"id": "f76bfe820ed3b20b", "src": "hda", "uuid": "1b8ef26f-453c-4fc7-bbd3-64c914cfd768"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.044 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat\n[main] Real time: 0.016 sec; CPU: 0.041 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat\n[main] Real time: 0.015 sec; CPU: 0.035 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat /galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat\n[main] Real time: 0.009 sec; CPU: 0.004 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.044 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat\n[main] Real time: 0.016 sec; CPU: 0.041 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat\n[main] Real time: 0.015 sec; CPU: 0.035 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/7/4/e/dataset_74e2fea9-fbb1-4152-82e0-669a6e59e45c.dat /galaxy/server/database/objects/2/4/2/dataset_24214749-c6a2-4963-95fa-4aa89b880b53.dat\n[main] Real time: 0.009 sec; CPU: 0.004 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:41:38", "plugin": "core", "name": "end_epoch", "raw_value": "1728110498.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:41:38", "plugin": "core", "name": "start_epoch", "raw_value": "1728110498.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-2", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 2, "time_seconds": 41.84341883659363, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "9584a994c964fa4e"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "7762f557498ed15a"}, "input_type|fastq_input2": {"src": "hda", "id": "6e285b05558ea69e"}, "input_type|input_type_selector": "paired", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "cc3b53475dde1ae6", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:42:19.429948", "update_time": "2024-10-05T06:42:33.337686", "galaxy_version": "24.1", "external_id": "gxy-j4m22", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/c/6/8/dataset_c68c08a5-5eb9-4de5-8ebd-442bdccbbbf7.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat' '/galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/2/0/e/dataset_20e76092-1b3b-405f-aa8d-b2349f597d98.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 0, \"adv_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 99, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 100, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 98, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "9584a994c964fa4e", "src": "hda", "uuid": "c68c08a5-5eb9-4de5-8ebd-442bdccbbbf7"}, "input_type|fastq_input1": {"id": "7762f557498ed15a", "src": "hda", "uuid": "d87cabdd-5815-4d4e-bec6-a83b26c0ac53"}, "input_type|fastq_input2": {"id": "6e285b05558ea69e", "src": "hda", "uuid": "b564f1e4-a38e-4390-99e9-9d6afa7faa63"}}, "outputs": {"bam_output": {"id": "67075bd0b9719099", "src": "hda", "uuid": "20e76092-1b3b-405f-aa8d-b2349f597d98"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.046 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat\n[main] Real time: 0.017 sec; CPU: 0.043 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat\n[main] Real time: 0.017 sec; CPU: 0.041 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat /galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat\n[main] Real time: 0.009 sec; CPU: 0.005 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.046 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat\n[main] Real time: 0.017 sec; CPU: 0.043 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat\n[main] Real time: 0.017 sec; CPU: 0.041 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/d/8/7/dataset_d87cabdd-5815-4d4e-bec6-a83b26c0ac53.dat /galaxy/server/database/objects/b/5/6/dataset_b564f1e4-a38e-4390-99e9-9d6afa7faa63.dat\n[main] Real time: 0.009 sec; CPU: 0.005 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:42:21", "plugin": "core", "name": "end_epoch", "raw_value": "1728110541.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:42:21", "plugin": "core", "name": "start_epoch", "raw_value": "1728110541.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-3", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 3, "time_seconds": 39.81927442550659, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "af11950b36af14f2"}, "reference_source|reference_source_selector": "history", "input_type|bam_input": {"src": "hda", "id": "0a03cf8dcdf43b0d"}, "input_type|input_type_selector": "paired_bam", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "717ae31659bceb0b", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:42:57.732024", "update_time": "2024-10-05T06:43:13.086294", "galaxy_version": "24.1", "external_id": "gxy-9rrhg", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/b/9/7/dataset_b979533e-58e2-4e94-8ec2-ee19d765c407.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" -b -1 'localref.fa' '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" -b -2 'localref.fa' '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' > second.sai && bwa sampe 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' '/galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/2/9/6/dataset_2969637e-0e3c-4114-b5ef-6a25d89da034.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "input_type": "{\"__current_case__\": 3, \"adv_bam_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"bam_input\": {\"values\": [{\"id\": 103, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired_bam\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 102, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "af11950b36af14f2", "src": "hda", "uuid": "b979533e-58e2-4e94-8ec2-ee19d765c407"}, "input_type|bam_input": {"id": "0a03cf8dcdf43b0d", "src": "hda", "uuid": "94692299-31f0-44f8-891b-5668ff72fa24"}}, "outputs": {"bam_output": {"id": "898527f9e130834e", "src": "hda", "uuid": "2969637e-0e3c-4114-b5ef-6a25d89da034"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.046 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.05 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -1 localref.fa /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat\n[main] Real time: 0.016 sec; CPU: 0.049 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -2 localref.fa /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat\n[main] Real time: 0.016 sec; CPU: 0.038 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat\n[main] Real time: 0.009 sec; CPU: 0.005 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.046 sec; CPU: 0.010 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.05 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -1 localref.fa /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat\n[main] Real time: 0.016 sec; CPU: 0.049 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 -b -2 localref.fa /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat\n[main] Real time: 0.016 sec; CPU: 0.038 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe localref.fa first.sai second.sai /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat /galaxy/server/database/objects/9/4/6/dataset_94692299-31f0-44f8-891b-5668ff72fa24.dat\n[main] Real time: 0.009 sec; CPU: 0.005 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:43:00", "plugin": "core", "name": "end_epoch", "raw_value": "1728110580.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:43:00", "plugin": "core", "name": "start_epoch", "raw_value": "1728110580.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "bwa/0.7.18-4", "has_data": true, "data": {"tool_id": "bwa", "tool_version": "0.7.18", "test_index": 4, "time_seconds": 43.756691694259644, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "d80facd9fa7307a4"}, "reference_source|reference_source_selector": "history", "input_type|fastq_input1": {"src": "hda", "id": "89258c891e92939f"}, "input_type|fastq_input2": {"src": "hda", "id": "5117f9fea7c22917"}, "input_type|input_type_selector": "paired", "rg|read_group_id_conditional|ID": "rg1", "rg|PL": "CAPILLARY", "rg|rg_selector": "set", "analysis_type|analysis_type_selector": "illumina"}, "job": {"model_class": "Job", "id": "ba22c5388737214c", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.18", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:43:42.175968", "update_time": "2024-10-05T06:43:56.881047", "galaxy_version": "24.1", "external_id": "gxy-ql45j", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; ln -s '/galaxy/server/database/objects/8/7/a/dataset_87ad91d1-3029-4d89-b0a0-901ce3fee026.dat' 'localref.fa' && bwa index 'localref.fa' && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat' > first.sai && bwa aln -t \"${GALAXY_SLOTS:-1}\" 'localref.fa' '/galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat' > second.sai && bwa sampe -r '@RG\\tID:rg1\\tPL:CAPILLARY' 'localref.fa' first.sai second.sai '/galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat' '/galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/galaxy/server/database/objects/7/c/d/dataset_7cd11f28-de6c-4ce2-a83c-2a96abd481cc.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"illumina\"}", "rg": "{\"CN\": null, \"DS\": null, \"DT\": null, \"FO\": null, \"KS\": null, \"PG\": null, \"PI\": \"\", \"PL\": \"CAPILLARY\", \"PU\": null, \"__current_case__\": 1, \"read_group_id_conditional\": {\"ID\": \"rg1\", \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_lb_conditional\": {\"LB\": null, \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_sm_conditional\": {\"SM\": \"\", \"__current_case__\": 1, \"do_auto_name\": false}, \"rg_selector\": \"set\"}", "input_type": "{\"__current_case__\": 0, \"adv_pe_options\": {\"__current_case__\": 1, \"adv_pe_options_selector\": \"do_not_set\"}, \"fastq_input1\": {\"values\": [{\"id\": 106, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 107, \"src\": \"hda\"}]}, \"input_type_selector\": \"paired\"}", "reference_source": "{\"__current_case__\": 1, \"index_a\": \"auto\", \"ref_file\": {\"values\": [{\"id\": 105, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "d80facd9fa7307a4", "src": "hda", "uuid": "87ad91d1-3029-4d89-b0a0-901ce3fee026"}, "input_type|fastq_input1": {"id": "89258c891e92939f", "src": "hda", "uuid": "e45bc374-f780-4282-b2ac-84be7b9f8e02"}, "input_type|fastq_input2": {"id": "5117f9fea7c22917", "src": "hda", "uuid": "fa43d733-ce86-4eb5-a23c-cfd9d110a8ac"}}, "outputs": {"bam_output": {"id": "87ef64afd1491f87", "src": "hda", "uuid": "7cd11f28-de6c-4ce2-a83c-2a96abd481cc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.041 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat\n[main] Real time: 0.016 sec; CPU: 0.042 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat\n[main] Real time: 0.014 sec; CPU: 0.034 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe -r @RG\\tID:rg1\\tPL:CAPILLARY localref.fa first.sai second.sai /galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat /galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat\n[main] Real time: 0.008 sec; CPU: 0.004 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bwa_index] Pack FASTA... 0.00 sec\n[bwa_index] Construct BWT for the packed sequence...\n[bwa_index] 0.00 seconds elapse.\n[bwa_index] Update BWT... 0.00 sec\n[bwa_index] Pack forward-only FASTA... 0.00 sec\n[bwa_index] Construct SA from BWT and Occ... 0.00 sec\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa index localref.fa\n[main] Real time: 0.041 sec; CPU: 0.009 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.04 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat\n[main] Real time: 0.016 sec; CPU: 0.042 sec\n[bwa_aln] 17bp reads: max_diff = 2\n[bwa_aln] 38bp reads: max_diff = 3\n[bwa_aln] 64bp reads: max_diff = 4\n[bwa_aln] 93bp reads: max_diff = 5\n[bwa_aln] 124bp reads: max_diff = 6\n[bwa_aln] 157bp reads: max_diff = 7\n[bwa_aln] 190bp reads: max_diff = 8\n[bwa_aln] 225bp reads: max_diff = 9\n[bwa_aln_core] calculate SA coordinate... 0.03 sec\n[bwa_aln_core] write to the disk... 0.00 sec\n[bwa_aln_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa aln -t 8 localref.fa /galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat\n[main] Real time: 0.014 sec; CPU: 0.034 sec\n[bwa_sai2sam_pe_core] convert to sequence coordinate... \n[infer_isize] fail to infer insert size: too few good pairs\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.\n[bwa_sai2sam_pe_core] align unmapped mate...\n[bwa_sai2sam_pe_core] time elapses: 0.00 sec\n[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec\n[bwa_sai2sam_pe_core] print alignments... 0.00 sec\n[bwa_sai2sam_pe_core] 100 sequences have been processed.\n[main] Version: 0.7.18-r1243-dirty\n[main] CMD: bwa sampe -r @RG\\tID:rg1\\tPL:CAPILLARY localref.fa first.sai second.sai /galaxy/server/database/objects/e/4/5/dataset_e45bc374-f780-4282-b2ac-84be7b9f8e02.dat /galaxy/server/database/objects/f/a/4/dataset_fa43d733-ce86-4eb5-a23c-cfd9d110a8ac.dat\n[main] Real time: 0.008 sec; CPU: 0.004 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:43:44", "plugin": "core", "name": "end_epoch", "raw_value": "1728110624.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:43:44", "plugin": "core", "name": "start_epoch", "raw_value": "1728110624.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "chromeister/1.5.a+galaxy1-0", "has_data": true, "data": {"tool_id": "chromeister", "tool_version": "1.5.a+galaxy1", "test_index": 0, "time_seconds": 94.08939027786255, "inputs": {"query": {"src": "hda", "id": "7a74bcdf8676f920"}, "db": {"src": "hda", "id": "4b347bb09f97d9c5"}, "dimension": "500"}, "job": {"model_class": "Job", "id": "6b6250d123b0f899", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:59:10.117101", "update_time": "2024-10-05T07:00:19.090214", "galaxy_version": "24.1", "external_id": "gxy-sxf2c", "handler": null, "job_runner_name": null, "command_line": "ln -s /galaxy/server/database/objects/0/6/0/dataset_060a8a6a-4362-444f-88bf-bd3b37622bfb.dat 'mycoplasma-232.fasta' && ln -s /galaxy/server/database/objects/9/9/2/dataset_992c6633-79b6-4f25-bf14-a64c675c5571.dat 'mycoplasma-7422.fasta' && CHROMEISTER -query 'mycoplasma-232.fasta' -db 'mycoplasma-7422.fasta' -dimension 500 -kmer 32 -diffuse 4 -out 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat && compute_score.R 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat 500 > '/galaxy/server/database/objects/e/2/d/dataset_e2df7c53-b5ef-4548-a518-6a5216251fa5.dat' && detect_events.py 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.raw.txt png && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.png '/galaxy/server/database/objects/d/b/4/dataset_db4131c0-9670-4c36-a016-da97cdfdf309.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat '/galaxy/server/database/objects/2/2/7/dataset_227fbfba-b5be-49cb-a187-8abbf7046cb3.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.filt.png '/galaxy/server/database/objects/2/6/3/dataset_2639f1bc-4384-4349-89f5-060be0dfac05.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.txt '/galaxy/server/database/objects/1/e/1/dataset_1e152f50-87d2-4f1f-85e1-b231ebd5e220.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.csv '/galaxy/server/database/objects/c/6/9/dataset_c69000eb-49b1-47da-ab6c-eb5d7c79c0d8.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pngevents": "true", "grid": "true", "diffuse": "\"4\"", "kmer": "\"32\"", "dimension": "\"500\""}, "inputs": {"query": {"id": "7a74bcdf8676f920", "src": "hda", "uuid": "060a8a6a-4362-444f-88bf-bd3b37622bfb"}, "db": {"id": "4b347bb09f97d9c5", "src": "hda", "uuid": "992c6633-79b6-4f25-bf14-a64c675c5571"}}, "outputs": {"output": {"id": "9235d1bf267d9842", "src": "hda", "uuid": "227fbfba-b5be-49cb-a187-8abbf7046cb3"}, "output_imagen": {"id": "ee8b53f1c73a3be3", "src": "hda", "uuid": "2639f1bc-4384-4349-89f5-060be0dfac05"}, "output_csv": {"id": "792db741c9fad5ad", "src": "hda", "uuid": "c69000eb-49b1-47da-ab6c-eb5d7c79c0d8"}, "output_events": {"id": "5f5fcbe8d2757cd0", "src": "hda", "uuid": "1e152f50-87d2-4f1f-85e1-b231ebd5e220"}, "output_events_png": {"id": "3d006627a75ec4a5", "src": "hda", "uuid": "db4131c0-9670-4c36-a016-da97cdfdf309"}, "output_score": {"id": "fcc885ce29ebb593", "src": "hda", "uuid": "e2df7c53-b5ef-4548-a518-6a5216251fa5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[INFO] Generating a 500x500 matrix\n[INFO] Loading database\n\r20%...\r40%...\r60%...\r80%...\r100%...[INFO] Database loaded and of length 898495.\n[INFO] Ratios: Q [1.785516e+03] D [1.796990e+03]. Lenghts: Q [892758] D [898495]\n[INFO] Pixel size: Q [5.600622e-04] D [5.564861e-04].\n[INFO] Computing absolute hit numbers.\n\r19%...\r39%...\r59%...\r79%...\r99%...Scanning hits table.\n\r0%...\r0%...\r0%...\r0%...\r0%...\r0%...\r1%...\r1%...\r1%...\r1%...\r1%...\r2%...\r2%...\r2%...\r2%...\r2%...\r3%...\r3%...\r3%...\r3%...\r3%...\r4%...\r4%...\r4%...\r4%...\r4%...\r5%...\r5%...\r5%...\r5%...\r5%...\r6%...\r6%...\r6%...\r6%...\r6%...\r7%...\r7%...\r7%...\r7%...\r7%...\r8%...\r8%...\r8%...\r8%...\r8%...\r9%...\r9%...\r9%...\r9%...\r9%...\r10%...\r10%...\r10%...\r10%...\r10%...\r11%...\r11%...\r11%...\r11%...\r11%...\r12%...\r12%...\r12%...\r12%...\r12%...\r13%...\r13%...\r13%...\r13%...\r13%...\r14%...\r14%...\r14%...\r14%...\r14%...\r15%...\r15%...\r15%...\r15%...\r15%...\r16%...\r16%...\r16%...\r16%...\r16%...\r17%...\r17%...\r17%...\r17%...\r17%...\r18%...\r18%...\r18%...\r18%...\r18%...\r19%...\r19%...\r19%...\r19%...\r19%...\r20%...\r20%...\r20%...\r20%...\r20%...\r21%...\r21%...\r21%...\r21%...\r21%...\r22%...\r22%...\r22%...\r22%...\r22%...\r23%...\r23%...\r23%...\r23%...\r23%...\r24%...\r24%...\r24%...\r24%...\r24%...\r25%...\r25%...\r25%...\r25%...\r25%...\r26%...\r26%...\r26%...\r26%...\r26%...\r27%...\r27%...\r27%...\r27%...\r27%...\r28%...\r28%...\r28%...\r28%...\r28%...\r29%...\r29%...\r29%...\r29%...\r29%...\r30%...\r30%...\r30%...\r30%...\r30%...\r31%...\r31%...\r31%...\r31%...\r31%...\r32%...\r32%...\r32%...\r32%...\r32%...\r33%...\r33%...\r33%...\r33%...\r33%...\r34%...\r34%...\r34%...\r34%...\r34%...\r35%...\r35%...\r35%...\r35%...\r35%...\r36%...\r36%...\r36%...\r36%...\r36%...\r37%...\r37%...\r37%...\r37%...\r37%...\r38%...\r38%...\r38%...\r38%...\r38%...\r39%...\r39%...\r39%...\r39%...\r39%...\r40%...\r40%...\r40%...\r40%...\r40%...\r41%...\r41%...\r41%...\r41%...\r41%...\r42%...\r42%...\r42%...\r42%...\r42%...\r43%...\r43%...\r43%...\r43%...\r43%...\r44%...\r44%...\r44%...\r44%...\r44%...\r45%...\r45%...\r45%...\r45%...\r45%...\r46%...\r46%...\r46%...\r46%...\r46%...\r47%...\r47%...\r47%...\r47%...\r47%...\r48%...\r48%...\r48%...\r48%...\r48%...\r49%...\r49%...\r49%...\r49%...\r49%...\r50%...\r50%...\r50%...\r50%...\r50%...\r51%...\r51%...\r51%...\r51%...\r51%...\r52%...\r52%...\r52%...\r52%...\r52%...\r53%...\r53%...\r53%...\r53%...\r53%...\r54%...\r54%...\r54%...\r54%...\r54%...\r55%...\r55%...\r55%...\r55%...\r55%...\r56%...\r56%...\r56%...\r56%...\r56%...\r57%...\r57%...\r57%...\r57%...\r57%...\r58%...\r58%...\r58%...\r58%...\r58%...\r59%...\r59%...\r59%...\r59%...\r59%...\r60%...\r60%...\r60%...\r60%...\r60%...\r61%...\r61%...\r61%...\r61%...\r61%...\r62%...\r62%...\r62%...\r62%...\r62%...\r63%...\r63%...\r63%...\r63%...\r63%...\r64%...\r64%...\r64%...\r64%...\r64%...\r65%...\r65%...\r65%...\r65%...\r65%...\r66%...\r66%...\r66%...\r66%...\r66%...\r67%...\r67%...\r67%...\r67%...\r67%...\r68%...\r68%...\r68%...\r68%...\r68%...\r69%...\r69%...\r69%...\r69%...\r69%...\r70%...\r70%...\r70%...\r70%...\r70%...\r71%...\r71%...\r71%...\r71%...\r71%...\r72%...\r72%...\r72%...\r72%...\r72%...\r73%...\r73%...\r73%...\r73%...\r73%...\r74%...\r74%...\r74%...\r74%...\r74%...\r75%...\r75%...\r75%...\r75%...\r75%...\r76%...\r76%...\r76%...\r76%...\r76%...\r77%...\r77%...\r77%...\r77%...\r77%...\r78%...\r78%...\r78%...\r78%...\r78%...\r79%...\r79%...\r79%...\r79%...\r79%...\r80%...\r80%...\r80%...\r80%...\r80%...\r81%...\r81%...\r81%...\r81%...\r81%...\r82%...\r82%...\r82%...\r82%...\r82%...\r83%...\r83%...\r83%...\r83%...\r83%...\r84%...\r84%...\r84%...\r84%...\r84%...\r85%...\r85%...\r85%...\r85%...\r85%...\r86%...\r86%...\r86%...\r86%...\r86%...\r87%...\r87%...\r87%...\r87%...\r87%...\r88%...\r88%...\r88%...\r88%...\r88%...\r89%...\r89%...\r89%...\r89%...\r89%...\r90%...\r90%...\r90%...\r90%...\r90%...\r91%...\r91%...\r91%...\r91%...\r91%...\r92%...\r92%...\r92%...\r92%...\r92%...\r93%...\r93%...\r93%...\r93%...\r93%...\r94%...\r94%...\r94%...\r94%...\r94%...\r95%...\r95%...\r95%...\r95%...\r95%...\r96%...\r96%...\r96%...\r96%...\r96%...\r97%...\r97%...\r97%...\r97%...\r97%...\r98%...\r98%...\r98%...\r98%...\r98%...\r99%...\r99%...\r99%...\r99%...\r99%...\n[INFO] Query length 892758.\n[INFO] Writing matrix.\n[INFO] Found 20083 unique hits for z = 4.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[INFO] Generating a 500x500 matrix\n[INFO] Loading database\n\r20%...\r40%...\r60%...\r80%...\r100%...[INFO] Database loaded and of length 898495.\n[INFO] Ratios: Q [1.785516e+03] D [1.796990e+03]. Lenghts: Q [892758] D [898495]\n[INFO] Pixel size: Q [5.600622e-04] D [5.564861e-04].\n[INFO] Computing absolute hit numbers.\n\r19%...\r39%...\r59%...\r79%...\r99%...Scanning hits table.\n\r0%...\r0%...\r0%...\r0%...\r0%...\r0%...\r1%...\r1%...\r1%...\r1%...\r1%...\r2%...\r2%...\r2%...\r2%...\r2%...\r3%...\r3%...\r3%...\r3%...\r3%...\r4%...\r4%...\r4%...\r4%...\r4%...\r5%...\r5%...\r5%...\r5%...\r5%...\r6%...\r6%...\r6%...\r6%...\r6%...\r7%...\r7%...\r7%...\r7%...\r7%...\r8%...\r8%...\r8%...\r8%...\r8%...\r9%...\r9%...\r9%...\r9%...\r9%...\r10%...\r10%...\r10%...\r10%...\r10%...\r11%...\r11%...\r11%...\r11%...\r11%...\r12%...\r12%...\r12%...\r12%...\r12%...\r13%...\r13%...\r13%...\r13%...\r13%...\r14%...\r14%...\r14%...\r14%...\r14%...\r15%...\r15%...\r15%...\r15%...\r15%...\r16%...\r16%...\r16%...\r16%...\r16%...\r17%...\r17%...\r17%...\r17%...\r17%...\r18%...\r18%...\r18%...\r18%...\r18%...\r19%...\r19%...\r19%...\r19%...\r19%...\r20%...\r20%...\r20%...\r20%...\r20%...\r21%...\r21%...\r21%...\r21%...\r21%...\r22%...\r22%...\r22%...\r22%...\r22%...\r23%...\r23%...\r23%...\r23%...\r23%...\r24%...\r24%...\r24%...\r24%...\r24%...\r25%...\r25%...\r25%...\r25%...\r25%...\r26%...\r26%...\r26%...\r26%...\r26%...\r27%...\r27%...\r27%...\r27%...\r27%...\r28%...\r28%...\r28%...\r28%...\r28%...\r29%...\r29%...\r29%...\r29%...\r29%...\r30%...\r30%...\r30%...\r30%...\r30%...\r31%...\r31%...\r31%...\r31%...\r31%...\r32%...\r32%...\r32%...\r32%...\r32%...\r33%...\r33%...\r33%...\r33%...\r33%...\r34%...\r34%...\r34%...\r34%...\r34%...\r35%...\r35%...\r35%...\r35%...\r35%...\r36%...\r36%...\r36%...\r36%...\r36%...\r37%...\r37%...\r37%...\r37%...\r37%...\r38%...\r38%...\r38%...\r38%...\r38%...\r39%...\r39%...\r39%...\r39%...\r39%...\r40%...\r40%...\r40%...\r40%...\r40%...\r41%...\r41%...\r41%...\r41%...\r41%...\r42%...\r42%...\r42%...\r42%...\r42%...\r43%...\r43%...\r43%...\r43%...\r43%...\r44%...\r44%...\r44%...\r44%...\r44%...\r45%...\r45%...\r45%...\r45%...\r45%...\r46%...\r46%...\r46%...\r46%...\r46%...\r47%...\r47%...\r47%...\r47%...\r47%...\r48%...\r48%...\r48%...\r48%...\r48%...\r49%...\r49%...\r49%...\r49%...\r49%...\r50%...\r50%...\r50%...\r50%...\r50%...\r51%...\r51%...\r51%...\r51%...\r51%...\r52%...\r52%...\r52%...\r52%...\r52%...\r53%...\r53%...\r53%...\r53%...\r53%...\r54%...\r54%...\r54%...\r54%...\r54%...\r55%...\r55%...\r55%...\r55%...\r55%...\r56%...\r56%...\r56%...\r56%...\r56%...\r57%...\r57%...\r57%...\r57%...\r57%...\r58%...\r58%...\r58%...\r58%...\r58%...\r59%...\r59%...\r59%...\r59%...\r59%...\r60%...\r60%...\r60%...\r60%...\r60%...\r61%...\r61%...\r61%...\r61%...\r61%...\r62%...\r62%...\r62%...\r62%...\r62%...\r63%...\r63%...\r63%...\r63%...\r63%...\r64%...\r64%...\r64%...\r64%...\r64%...\r65%...\r65%...\r65%...\r65%...\r65%...\r66%...\r66%...\r66%...\r66%...\r66%...\r67%...\r67%...\r67%...\r67%...\r67%...\r68%...\r68%...\r68%...\r68%...\r68%...\r69%...\r69%...\r69%...\r69%...\r69%...\r70%...\r70%...\r70%...\r70%...\r70%...\r71%...\r71%...\r71%...\r71%...\r71%...\r72%...\r72%...\r72%...\r72%...\r72%...\r73%...\r73%...\r73%...\r73%...\r73%...\r74%...\r74%...\r74%...\r74%...\r74%...\r75%...\r75%...\r75%...\r75%...\r75%...\r76%...\r76%...\r76%...\r76%...\r76%...\r77%...\r77%...\r77%...\r77%...\r77%...\r78%...\r78%...\r78%...\r78%...\r78%...\r79%...\r79%...\r79%...\r79%...\r79%...\r80%...\r80%...\r80%...\r80%...\r80%...\r81%...\r81%...\r81%...\r81%...\r81%...\r82%...\r82%...\r82%...\r82%...\r82%...\r83%...\r83%...\r83%...\r83%...\r83%...\r84%...\r84%...\r84%...\r84%...\r84%...\r85%...\r85%...\r85%...\r85%...\r85%...\r86%...\r86%...\r86%...\r86%...\r86%...\r87%...\r87%...\r87%...\r87%...\r87%...\r88%...\r88%...\r88%...\r88%...\r88%...\r89%...\r89%...\r89%...\r89%...\r89%...\r90%...\r90%...\r90%...\r90%...\r90%...\r91%...\r91%...\r91%...\r91%...\r91%...\r92%...\r92%...\r92%...\r92%...\r92%...\r93%...\r93%...\r93%...\r93%...\r93%...\r94%...\r94%...\r94%...\r94%...\r94%...\r95%...\r95%...\r95%...\r95%...\r95%...\r96%...\r96%...\r96%...\r96%...\r96%...\r97%...\r97%...\r97%...\r97%...\r97%...\r98%...\r98%...\r98%...\r98%...\r98%...\r99%...\r99%...\r99%...\r99%...\r99%...\n[INFO] Query length 892758.\n[INFO] Writing matrix.\n[INFO] Found 20083 unique hits for z = 4.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "12 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "12.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:59:53", "plugin": "core", "name": "end_epoch", "raw_value": "1728111593.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:59:41", "plugin": "core", "name": "start_epoch", "raw_value": "1728111581.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "chromeister/1.5.a+galaxy1-1", "has_data": true, "data": {"tool_id": "chromeister", "tool_version": "1.5.a+galaxy1", "test_index": 1, "time_seconds": 75.69501209259033, "inputs": {"query": {"src": "hda", "id": "3ccad63739fcba4a"}, "db": {"src": "hda", "id": "0bbcad2f82f641d1"}, "kmer": "16", "diffuse": "3", "grid": false}, "job": {"model_class": "Job", "id": "0e0dc0e56adbe5f4", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:00:45.156330", "update_time": "2024-10-05T07:01:34.885098", "galaxy_version": "24.1", "external_id": "gxy-jjs5f", "handler": null, "job_runner_name": null, "command_line": "ln -s /galaxy/server/database/objects/2/9/0/dataset_29085765-63a5-45ce-af65-700da8961e1b.dat 'mycoplasma-232.fasta' && ln -s /galaxy/server/database/objects/e/5/7/dataset_e5711e30-b370-4ca7-b0a0-cf50ca64030b.dat 'mycoplasma-7422.fasta' && CHROMEISTER -query 'mycoplasma-232.fasta' -db 'mycoplasma-7422.fasta' -dimension 1000 -kmer 16 -diffuse 3 -out 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat && compute_score-nogrid.R 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat 1000 > '/galaxy/server/database/objects/b/e/d/dataset_bed2ae46-c29e-489a-bda4-78a6024d95a9.dat' && detect_events.py 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.raw.txt png && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.png '/galaxy/server/database/objects/e/5/a/dataset_e5a3b465-352e-442f-bfbd-b45319ac8dbd.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat '/galaxy/server/database/objects/8/e/3/dataset_8e38f460-ef91-437f-81bb-6e48055db2aa.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.filt.png '/galaxy/server/database/objects/8/7/7/dataset_87746d12-fb3a-4697-8a32-15b255e28b38.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.txt '/galaxy/server/database/objects/e/a/e/dataset_eae87982-91a0-44a2-8282-aec6d17e0bb7.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.csv '/galaxy/server/database/objects/3/9/d/dataset_39deb19c-8550-4bda-b429-cb30d2bfbf54.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pngevents": "true", "grid": "false", "diffuse": "\"3\"", "kmer": "\"16\"", "dimension": "\"1000\""}, "inputs": {"query": {"id": "3ccad63739fcba4a", "src": "hda", "uuid": "29085765-63a5-45ce-af65-700da8961e1b"}, "db": {"id": "0bbcad2f82f641d1", "src": "hda", "uuid": "e5711e30-b370-4ca7-b0a0-cf50ca64030b"}}, "outputs": {"output": {"id": "8a63ec791686ed64", "src": "hda", "uuid": "8e38f460-ef91-437f-81bb-6e48055db2aa"}, "output_imagen": {"id": "e562dfcc41be1b87", "src": "hda", "uuid": "87746d12-fb3a-4697-8a32-15b255e28b38"}, "output_csv": {"id": "ed4077bd01072e1b", "src": "hda", "uuid": "39deb19c-8550-4bda-b429-cb30d2bfbf54"}, "output_events": {"id": "d28be923de36a42e", "src": "hda", "uuid": "eae87982-91a0-44a2-8282-aec6d17e0bb7"}, "output_events_png": {"id": "e7be7103c96020d3", "src": "hda", "uuid": "e5a3b465-352e-442f-bfbd-b45319ac8dbd"}, "output_score": {"id": "5b758cb367bc2ec8", "src": "hda", "uuid": "bed2ae46-c29e-489a-bda4-78a6024d95a9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[INFO] Generating a 1000x1000 matrix\n[INFO] Loading database\n\r20%...\r40%...\r60%...\r80%...\r100%...[INFO] Database loaded and of length 898495.\n[INFO] Ratios: Q [8.927580e+02] D [8.984950e+02]. Lenghts: Q [892758] D [898495]\n[INFO] Pixel size: Q [1.120124e-03] D [1.112972e-03].\n[INFO] Computing absolute hit numbers.\n\r19%...\r39%...\r59%...\r79%...\r99%...Scanning hits table.\n\r0%...\r0%...\r0%...\r0%...\r0%...\r0%...\r1%...\r1%...\r1%...\r1%...\r1%...\r2%...\r2%...\r2%...\r2%...\r2%...\r3%...\r3%...\r3%...\r3%...\r3%...\r4%...\r4%...\r4%...\r4%...\r4%...\r5%...\r5%...\r5%...\r5%...\r5%...\r6%...\r6%...\r6%...\r6%...\r6%...\r7%...\r7%...\r7%...\r7%...\r7%...\r8%...\r8%...\r8%...\r8%...\r8%...\r9%...\r9%...\r9%...\r9%...\r9%...\r10%...\r10%...\r10%...\r10%...\r10%...\r11%...\r11%...\r11%...\r11%...\r11%...\r12%...\r12%...\r12%...\r12%...\r12%...\r13%...\r13%...\r13%...\r13%...\r13%...\r14%...\r14%...\r14%...\r14%...\r14%...\r15%...\r15%...\r15%...\r15%...\r15%...\r16%...\r16%...\r16%...\r16%...\r16%...\r17%...\r17%...\r17%...\r17%...\r17%...\r18%...\r18%...\r18%...\r18%...\r18%...\r19%...\r19%...\r19%...\r19%...\r19%...\r20%...\r20%...\r20%...\r20%...\r20%...\r21%...\r21%...\r21%...\r21%...\r21%...\r22%...\r22%...\r22%...\r22%...\r22%...\r23%...\r23%...\r23%...\r23%...\r23%...\r24%...\r24%...\r24%...\r24%...\r24%...\r25%...\r25%...\r25%...\r25%...\r25%...\r26%...\r26%...\r26%...\r26%...\r26%...\r27%...\r27%...\r27%...\r27%...\r27%...\r28%...\r28%...\r28%...\r28%...\r28%...\r29%...\r29%...\r29%...\r29%...\r29%...\r30%...\r30%...\r30%...\r30%...\r30%...\r31%...\r31%...\r31%...\r31%...\r31%...\r32%...\r32%...\r32%...\r32%...\r32%...\r33%...\r33%...\r33%...\r33%...\r33%...\r34%...\r34%...\r34%...\r34%...\r34%...\r35%...\r35%...\r35%...\r35%...\r35%...\r36%...\r36%...\r36%...\r36%...\r36%...\r37%...\r37%...\r37%...\r37%...\r37%...\r38%...\r38%...\r38%...\r38%...\r38%...\r39%...\r39%...\r39%...\r39%...\r39%...\r40%...\r40%...\r40%...\r40%...\r40%...\r41%...\r41%...\r41%...\r41%...\r41%...\r42%...\r42%...\r42%...\r42%...\r42%...\r43%...\r43%...\r43%...\r43%...\r43%...\r44%...\r44%...\r44%...\r44%...\r44%...\r45%...\r45%...\r45%...\r45%...\r45%...\r46%...\r46%...\r46%...\r46%...\r46%...\r47%...\r47%...\r47%...\r47%...\r47%...\r48%...\r48%...\r48%...\r48%...\r48%...\r49%...\r49%...\r49%...\r49%...\r49%...\r50%...\r50%...\r50%...\r50%...\r50%...\r51%...\r51%...\r51%...\r51%...\r51%...\r52%...\r52%...\r52%...\r52%...\r52%...\r53%...\r53%...\r53%...\r53%...\r53%...\r54%...\r54%...\r54%...\r54%...\r54%...\r55%...\r55%...\r55%...\r55%...\r55%...\r56%...\r56%...\r56%...\r56%...\r56%...\r57%...\r57%...\r57%...\r57%...\r57%...\r58%...\r58%...\r58%...\r58%...\r58%...\r59%...\r59%...\r59%...\r59%...\r59%...\r60%...\r60%...\r60%...\r60%...\r60%...\r61%...\r61%...\r61%...\r61%...\r61%...\r62%...\r62%...\r62%...\r62%...\r62%...\r63%...\r63%...\r63%...\r63%...\r63%...\r64%...\r64%...\r64%...\r64%...\r64%...\r65%...\r65%...\r65%...\r65%...\r65%...\r66%...\r66%...\r66%...\r66%...\r66%...\r67%...\r67%...\r67%...\r67%...\r67%...\r68%...\r68%...\r68%...\r68%...\r68%...\r69%...\r69%...\r69%...\r69%...\r69%...\r70%...\r70%...\r70%...\r70%...\r70%...\r71%...\r71%...\r71%...\r71%...\r71%...\r72%...\r72%...\r72%...\r72%...\r72%...\r73%...\r73%...\r73%...\r73%...\r73%...\r74%...\r74%...\r74%...\r74%...\r74%...\r75%...\r75%...\r75%...\r75%...\r75%...\r76%...\r76%...\r76%...\r76%...\r76%...\r77%...\r77%...\r77%...\r77%...\r77%...\r78%...\r78%...\r78%...\r78%...\r78%...\r79%...\r79%...\r79%...\r79%...\r79%...\r80%...\r80%...\r80%...\r80%...\r80%...\r81%...\r81%...\r81%...\r81%...\r81%...\r82%...\r82%...\r82%...\r82%...\r82%...\r83%...\r83%...\r83%...\r83%...\r83%...\r84%...\r84%...\r84%...\r84%...\r84%...\r85%...\r85%...\r85%...\r85%...\r85%...\r86%...\r86%...\r86%...\r86%...\r86%...\r87%...\r87%...\r87%...\r87%...\r87%...\r88%...\r88%...\r88%...\r88%...\r88%...\r89%...\r89%...\r89%...\r89%...\r89%...\r90%...\r90%...\r90%...\r90%...\r90%...\r91%...\r91%...\r91%...\r91%...\r91%...\r92%...\r92%...\r92%...\r92%...\r92%...\r93%...\r93%...\r93%...\r93%...\r93%...\r94%...\r94%...\r94%...\r94%...\r94%...\r95%...\r95%...\r95%...\r95%...\r95%...\r96%...\r96%...\r96%...\r96%...\r96%...\r97%...\r97%...\r97%...\r97%...\r97%...\r98%...\r98%...\r98%...\r98%...\r98%...\r99%...\r99%...\r99%...\r99%...\r99%...\n[INFO] Query length 892758.\n[INFO] Writing matrix.\n[INFO] Found 36133 unique hits for z = 3.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[INFO] Generating a 1000x1000 matrix\n[INFO] Loading database\n\r20%...\r40%...\r60%...\r80%...\r100%...[INFO] Database loaded and of length 898495.\n[INFO] Ratios: Q [8.927580e+02] D [8.984950e+02]. Lenghts: Q [892758] D [898495]\n[INFO] Pixel size: Q [1.120124e-03] D [1.112972e-03].\n[INFO] Computing absolute hit numbers.\n\r19%...\r39%...\r59%...\r79%...\r99%...Scanning hits table.\n\r0%...\r0%...\r0%...\r0%...\r0%...\r0%...\r1%...\r1%...\r1%...\r1%...\r1%...\r2%...\r2%...\r2%...\r2%...\r2%...\r3%...\r3%...\r3%...\r3%...\r3%...\r4%...\r4%...\r4%...\r4%...\r4%...\r5%...\r5%...\r5%...\r5%...\r5%...\r6%...\r6%...\r6%...\r6%...\r6%...\r7%...\r7%...\r7%...\r7%...\r7%...\r8%...\r8%...\r8%...\r8%...\r8%...\r9%...\r9%...\r9%...\r9%...\r9%...\r10%...\r10%...\r10%...\r10%...\r10%...\r11%...\r11%...\r11%...\r11%...\r11%...\r12%...\r12%...\r12%...\r12%...\r12%...\r13%...\r13%...\r13%...\r13%...\r13%...\r14%...\r14%...\r14%...\r14%...\r14%...\r15%...\r15%...\r15%...\r15%...\r15%...\r16%...\r16%...\r16%...\r16%...\r16%...\r17%...\r17%...\r17%...\r17%...\r17%...\r18%...\r18%...\r18%...\r18%...\r18%...\r19%...\r19%...\r19%...\r19%...\r19%...\r20%...\r20%...\r20%...\r20%...\r20%...\r21%...\r21%...\r21%...\r21%...\r21%...\r22%...\r22%...\r22%...\r22%...\r22%...\r23%...\r23%...\r23%...\r23%...\r23%...\r24%...\r24%...\r24%...\r24%...\r24%...\r25%...\r25%...\r25%...\r25%...\r25%...\r26%...\r26%...\r26%...\r26%...\r26%...\r27%...\r27%...\r27%...\r27%...\r27%...\r28%...\r28%...\r28%...\r28%...\r28%...\r29%...\r29%...\r29%...\r29%...\r29%...\r30%...\r30%...\r30%...\r30%...\r30%...\r31%...\r31%...\r31%...\r31%...\r31%...\r32%...\r32%...\r32%...\r32%...\r32%...\r33%...\r33%...\r33%...\r33%...\r33%...\r34%...\r34%...\r34%...\r34%...\r34%...\r35%...\r35%...\r35%...\r35%...\r35%...\r36%...\r36%...\r36%...\r36%...\r36%...\r37%...\r37%...\r37%...\r37%...\r37%...\r38%...\r38%...\r38%...\r38%...\r38%...\r39%...\r39%...\r39%...\r39%...\r39%...\r40%...\r40%...\r40%...\r40%...\r40%...\r41%...\r41%...\r41%...\r41%...\r41%...\r42%...\r42%...\r42%...\r42%...\r42%...\r43%...\r43%...\r43%...\r43%...\r43%...\r44%...\r44%...\r44%...\r44%...\r44%...\r45%...\r45%...\r45%...\r45%...\r45%...\r46%...\r46%...\r46%...\r46%...\r46%...\r47%...\r47%...\r47%...\r47%...\r47%...\r48%...\r48%...\r48%...\r48%...\r48%...\r49%...\r49%...\r49%...\r49%...\r49%...\r50%...\r50%...\r50%...\r50%...\r50%...\r51%...\r51%...\r51%...\r51%...\r51%...\r52%...\r52%...\r52%...\r52%...\r52%...\r53%...\r53%...\r53%...\r53%...\r53%...\r54%...\r54%...\r54%...\r54%...\r54%...\r55%...\r55%...\r55%...\r55%...\r55%...\r56%...\r56%...\r56%...\r56%...\r56%...\r57%...\r57%...\r57%...\r57%...\r57%...\r58%...\r58%...\r58%...\r58%...\r58%...\r59%...\r59%...\r59%...\r59%...\r59%...\r60%...\r60%...\r60%...\r60%...\r60%...\r61%...\r61%...\r61%...\r61%...\r61%...\r62%...\r62%...\r62%...\r62%...\r62%...\r63%...\r63%...\r63%...\r63%...\r63%...\r64%...\r64%...\r64%...\r64%...\r64%...\r65%...\r65%...\r65%...\r65%...\r65%...\r66%...\r66%...\r66%...\r66%...\r66%...\r67%...\r67%...\r67%...\r67%...\r67%...\r68%...\r68%...\r68%...\r68%...\r68%...\r69%...\r69%...\r69%...\r69%...\r69%...\r70%...\r70%...\r70%...\r70%...\r70%...\r71%...\r71%...\r71%...\r71%...\r71%...\r72%...\r72%...\r72%...\r72%...\r72%...\r73%...\r73%...\r73%...\r73%...\r73%...\r74%...\r74%...\r74%...\r74%...\r74%...\r75%...\r75%...\r75%...\r75%...\r75%...\r76%...\r76%...\r76%...\r76%...\r76%...\r77%...\r77%...\r77%...\r77%...\r77%...\r78%...\r78%...\r78%...\r78%...\r78%...\r79%...\r79%...\r79%...\r79%...\r79%...\r80%...\r80%...\r80%...\r80%...\r80%...\r81%...\r81%...\r81%...\r81%...\r81%...\r82%...\r82%...\r82%...\r82%...\r82%...\r83%...\r83%...\r83%...\r83%...\r83%...\r84%...\r84%...\r84%...\r84%...\r84%...\r85%...\r85%...\r85%...\r85%...\r85%...\r86%...\r86%...\r86%...\r86%...\r86%...\r87%...\r87%...\r87%...\r87%...\r87%...\r88%...\r88%...\r88%...\r88%...\r88%...\r89%...\r89%...\r89%...\r89%...\r89%...\r90%...\r90%...\r90%...\r90%...\r90%...\r91%...\r91%...\r91%...\r91%...\r91%...\r92%...\r92%...\r92%...\r92%...\r92%...\r93%...\r93%...\r93%...\r93%...\r93%...\r94%...\r94%...\r94%...\r94%...\r94%...\r95%...\r95%...\r95%...\r95%...\r95%...\r96%...\r96%...\r96%...\r96%...\r96%...\r97%...\r97%...\r97%...\r97%...\r97%...\r98%...\r98%...\r98%...\r98%...\r98%...\r99%...\r99%...\r99%...\r99%...\r99%...\n[INFO] Query length 892758.\n[INFO] Writing matrix.\n[INFO] Found 36133 unique hits for z = 3.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "35 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "35.0000000"}, {"title": "Job End Time", "value": "2024-10-05 07:01:21", "plugin": "core", "name": "end_epoch", "raw_value": "1728111681.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 07:00:46", "plugin": "core", "name": "start_epoch", "raw_value": "1728111646.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "chromeister/1.5.a+galaxy1-2", "has_data": true, "data": {"tool_id": "chromeister", "tool_version": "1.5.a+galaxy1", "test_index": 2, "time_seconds": 22.949461221694946, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "chromeister/1.5.a+galaxy1-3", "has_data": true, "data": {"tool_id": "chromeister", "tool_version": "1.5.a+galaxy1", "test_index": 3, "time_seconds": 74.18357706069946, "inputs": {"query": {"src": "hda", "id": "8a8e26370326e199"}, "db": {"src": "hda", "id": "d6aafe1256b5048f"}, "dimension": "1000", "kmer": "32", "diffuse": "4", "grid": false, "pngevents": true}, "job": {"model_class": "Job", "id": "aeb10c489f7558cc", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:02:23.229375", "update_time": "2024-10-05T07:03:13.425402", "galaxy_version": "24.1", "external_id": "gxy-xwbzk", "handler": null, "job_runner_name": null, "command_line": "ln -s /galaxy/server/database/objects/f/c/5/dataset_fc52f6db-4dd1-4b05-a701-0c03b3aef759.dat 'mycoplasma-232.fasta' && ln -s /galaxy/server/database/objects/6/8/b/dataset_68b24101-70a7-4a47-bd9f-a6877d17388d.dat 'mycoplasma-7422.fasta' && CHROMEISTER -query 'mycoplasma-232.fasta' -db 'mycoplasma-7422.fasta' -dimension 1000 -kmer 32 -diffuse 4 -out 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat && compute_score-nogrid.R 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat 1000 > '/galaxy/server/database/objects/7/d/2/dataset_7d283864-923c-4790-a6f6-c45520ab1efc.dat' && detect_events.py 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.raw.txt png && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.png '/galaxy/server/database/objects/f/e/7/dataset_fe77d406-3e94-426f-992c-1291a345685d.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat '/galaxy/server/database/objects/6/0/c/dataset_60c59b16-0be7-46f0-a378-d3519a9cf604.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.filt.png '/galaxy/server/database/objects/c/7/9/dataset_c79b0f12-e56e-4585-8adc-15c30fe5ca5b.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.events.txt '/galaxy/server/database/objects/a/d/2/dataset_ad21fc79-a73f-40ce-b827-8809c2c3da7e.dat' && mv 'mycoplasma-232.fasta'-'mycoplasma-7422.fasta'.mat.csv '/galaxy/server/database/objects/0/5/7/dataset_057bcd25-4cf7-42df-97ff-565fb29ba395.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pngevents": "true", "grid": "false", "diffuse": "\"4\"", "kmer": "\"32\"", "dimension": "\"1000\""}, "inputs": {"query": {"id": "8a8e26370326e199", "src": "hda", "uuid": "fc52f6db-4dd1-4b05-a701-0c03b3aef759"}, "db": {"id": "d6aafe1256b5048f", "src": "hda", "uuid": "68b24101-70a7-4a47-bd9f-a6877d17388d"}}, "outputs": {"output": {"id": "d0c0f5ff8e863b33", "src": "hda", "uuid": "60c59b16-0be7-46f0-a378-d3519a9cf604"}, "output_imagen": {"id": "8758d679a4a680e2", "src": "hda", "uuid": "c79b0f12-e56e-4585-8adc-15c30fe5ca5b"}, "output_csv": {"id": "b467b06e412b84dd", "src": "hda", "uuid": "057bcd25-4cf7-42df-97ff-565fb29ba395"}, "output_events": {"id": "5f2f38b7a2129db1", "src": "hda", "uuid": "ad21fc79-a73f-40ce-b827-8809c2c3da7e"}, "output_events_png": {"id": "788ded667c5ddc06", "src": "hda", "uuid": "fe77d406-3e94-426f-992c-1291a345685d"}, "output_score": {"id": "10b11da8087d5e9f", "src": "hda", "uuid": "7d283864-923c-4790-a6f6-c45520ab1efc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[INFO] Generating a 1000x1000 matrix\n[INFO] Loading database\n\r20%...\r40%...\r60%...\r80%...\r100%...[INFO] Database loaded and of length 898495.\n[INFO] Ratios: Q [8.927580e+02] D [8.984950e+02]. Lenghts: Q [892758] D [898495]\n[INFO] Pixel size: Q [1.120124e-03] D [1.112972e-03].\n[INFO] Computing absolute hit numbers.\n\r19%...\r39%...\r59%...\r79%...\r99%...Scanning hits table.\n\r0%...\r0%...\r0%...\r0%...\r0%...\r0%...\r1%...\r1%...\r1%...\r1%...\r1%...\r2%...\r2%...\r2%...\r2%...\r2%...\r3%...\r3%...\r3%...\r3%...\r3%...\r4%...\r4%...\r4%...\r4%...\r4%...\r5%...\r5%...\r5%...\r5%...\r5%...\r6%...\r6%...\r6%...\r6%...\r6%...\r7%...\r7%...\r7%...\r7%...\r7%...\r8%...\r8%...\r8%...\r8%...\r8%...\r9%...\r9%...\r9%...\r9%...\r9%...\r10%...\r10%...\r10%...\r10%...\r10%...\r11%...\r11%...\r11%...\r11%...\r11%...\r12%...\r12%...\r12%...\r12%...\r12%...\r13%...\r13%...\r13%...\r13%...\r13%...\r14%...\r14%...\r14%...\r14%...\r14%...\r15%...\r15%...\r15%...\r15%...\r15%...\r16%...\r16%...\r16%...\r16%...\r16%...\r17%...\r17%...\r17%...\r17%...\r17%...\r18%...\r18%...\r18%...\r18%...\r18%...\r19%...\r19%...\r19%...\r19%...\r19%...\r20%...\r20%...\r20%...\r20%...\r20%...\r21%...\r21%...\r21%...\r21%...\r21%...\r22%...\r22%...\r22%...\r22%...\r22%...\r23%...\r23%...\r23%...\r23%...\r23%...\r24%...\r24%...\r24%...\r24%...\r24%...\r25%...\r25%...\r25%...\r25%...\r25%...\r26%...\r26%...\r26%...\r26%...\r26%...\r27%...\r27%...\r27%...\r27%...\r27%...\r28%...\r28%...\r28%...\r28%...\r28%...\r29%...\r29%...\r29%...\r29%...\r29%...\r30%...\r30%...\r30%...\r30%...\r30%...\r31%...\r31%...\r31%...\r31%...\r31%...\r32%...\r32%...\r32%...\r32%...\r32%...\r33%...\r33%...\r33%...\r33%...\r33%...\r34%...\r34%...\r34%...\r34%...\r34%...\r35%...\r35%...\r35%...\r35%...\r35%...\r36%...\r36%...\r36%...\r36%...\r36%...\r37%...\r37%...\r37%...\r37%...\r37%...\r38%...\r38%...\r38%...\r38%...\r38%...\r39%...\r39%...\r39%...\r39%...\r39%...\r40%...\r40%...\r40%...\r40%...\r40%...\r41%...\r41%...\r41%...\r41%...\r41%...\r42%...\r42%...\r42%...\r42%...\r42%...\r43%...\r43%...\r43%...\r43%...\r43%...\r44%...\r44%...\r44%...\r44%...\r44%...\r45%...\r45%...\r45%...\r45%...\r45%...\r46%...\r46%...\r46%...\r46%...\r46%...\r47%...\r47%...\r47%...\r47%...\r47%...\r48%...\r48%...\r48%...\r48%...\r48%...\r49%...\r49%...\r49%...\r49%...\r49%...\r50%...\r50%...\r50%...\r50%...\r50%...\r51%...\r51%...\r51%...\r51%...\r51%...\r52%...\r52%...\r52%...\r52%...\r52%...\r53%...\r53%...\r53%...\r53%...\r53%...\r54%...\r54%...\r54%...\r54%...\r54%...\r55%...\r55%...\r55%...\r55%...\r55%...\r56%...\r56%...\r56%...\r56%...\r56%...\r57%...\r57%...\r57%...\r57%...\r57%...\r58%...\r58%...\r58%...\r58%...\r58%...\r59%...\r59%...\r59%...\r59%...\r59%...\r60%...\r60%...\r60%...\r60%...\r60%...\r61%...\r61%...\r61%...\r61%...\r61%...\r62%...\r62%...\r62%...\r62%...\r62%...\r63%...\r63%...\r63%...\r63%...\r63%...\r64%...\r64%...\r64%...\r64%...\r64%...\r65%...\r65%...\r65%...\r65%...\r65%...\r66%...\r66%...\r66%...\r66%...\r66%...\r67%...\r67%...\r67%...\r67%...\r67%...\r68%...\r68%...\r68%...\r68%...\r68%...\r69%...\r69%...\r69%...\r69%...\r69%...\r70%...\r70%...\r70%...\r70%...\r70%...\r71%...\r71%...\r71%...\r71%...\r71%...\r72%...\r72%...\r72%...\r72%...\r72%...\r73%...\r73%...\r73%...\r73%...\r73%...\r74%...\r74%...\r74%...\r74%...\r74%...\r75%...\r75%...\r75%...\r75%...\r75%...\r76%...\r76%...\r76%...\r76%...\r76%...\r77%...\r77%...\r77%...\r77%...\r77%...\r78%...\r78%...\r78%...\r78%...\r78%...\r79%...\r79%...\r79%...\r79%...\r79%...\r80%...\r80%...\r80%...\r80%...\r80%...\r81%...\r81%...\r81%...\r81%...\r81%...\r82%...\r82%...\r82%...\r82%...\r82%...\r83%...\r83%...\r83%...\r83%...\r83%...\r84%...\r84%...\r84%...\r84%...\r84%...\r85%...\r85%...\r85%...\r85%...\r85%...\r86%...\r86%...\r86%...\r86%...\r86%...\r87%...\r87%...\r87%...\r87%...\r87%...\r88%...\r88%...\r88%...\r88%...\r88%...\r89%...\r89%...\r89%...\r89%...\r89%...\r90%...\r90%...\r90%...\r90%...\r90%...\r91%...\r91%...\r91%...\r91%...\r91%...\r92%...\r92%...\r92%...\r92%...\r92%...\r93%...\r93%...\r93%...\r93%...\r93%...\r94%...\r94%...\r94%...\r94%...\r94%...\r95%...\r95%...\r95%...\r95%...\r95%...\r96%...\r96%...\r96%...\r96%...\r96%...\r97%...\r97%...\r97%...\r97%...\r97%...\r98%...\r98%...\r98%...\r98%...\r98%...\r99%...\r99%...\r99%...\r99%...\r99%...\n[INFO] Query length 892758.\n[INFO] Writing matrix.\n[INFO] Found 20083 unique hits for z = 4.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[INFO] Generating a 1000x1000 matrix\n[INFO] Loading database\n\r20%...\r40%...\r60%...\r80%...\r100%...[INFO] Database loaded and of length 898495.\n[INFO] Ratios: Q [8.927580e+02] D [8.984950e+02]. Lenghts: Q [892758] D [898495]\n[INFO] Pixel size: Q [1.120124e-03] D [1.112972e-03].\n[INFO] Computing absolute hit numbers.\n\r19%...\r39%...\r59%...\r79%...\r99%...Scanning hits table.\n\r0%...\r0%...\r0%...\r0%...\r0%...\r0%...\r1%...\r1%...\r1%...\r1%...\r1%...\r2%...\r2%...\r2%...\r2%...\r2%...\r3%...\r3%...\r3%...\r3%...\r3%...\r4%...\r4%...\r4%...\r4%...\r4%...\r5%...\r5%...\r5%...\r5%...\r5%...\r6%...\r6%...\r6%...\r6%...\r6%...\r7%...\r7%...\r7%...\r7%...\r7%...\r8%...\r8%...\r8%...\r8%...\r8%...\r9%...\r9%...\r9%...\r9%...\r9%...\r10%...\r10%...\r10%...\r10%...\r10%...\r11%...\r11%...\r11%...\r11%...\r11%...\r12%...\r12%...\r12%...\r12%...\r12%...\r13%...\r13%...\r13%...\r13%...\r13%...\r14%...\r14%...\r14%...\r14%...\r14%...\r15%...\r15%...\r15%...\r15%...\r15%...\r16%...\r16%...\r16%...\r16%...\r16%...\r17%...\r17%...\r17%...\r17%...\r17%...\r18%...\r18%...\r18%...\r18%...\r18%...\r19%...\r19%...\r19%...\r19%...\r19%...\r20%...\r20%...\r20%...\r20%...\r20%...\r21%...\r21%...\r21%...\r21%...\r21%...\r22%...\r22%...\r22%...\r22%...\r22%...\r23%...\r23%...\r23%...\r23%...\r23%...\r24%...\r24%...\r24%...\r24%...\r24%...\r25%...\r25%...\r25%...\r25%...\r25%...\r26%...\r26%...\r26%...\r26%...\r26%...\r27%...\r27%...\r27%...\r27%...\r27%...\r28%...\r28%...\r28%...\r28%...\r28%...\r29%...\r29%...\r29%...\r29%...\r29%...\r30%...\r30%...\r30%...\r30%...\r30%...\r31%...\r31%...\r31%...\r31%...\r31%...\r32%...\r32%...\r32%...\r32%...\r32%...\r33%...\r33%...\r33%...\r33%...\r33%...\r34%...\r34%...\r34%...\r34%...\r34%...\r35%...\r35%...\r35%...\r35%...\r35%...\r36%...\r36%...\r36%...\r36%...\r36%...\r37%...\r37%...\r37%...\r37%...\r37%...\r38%...\r38%...\r38%...\r38%...\r38%...\r39%...\r39%...\r39%...\r39%...\r39%...\r40%...\r40%...\r40%...\r40%...\r40%...\r41%...\r41%...\r41%...\r41%...\r41%...\r42%...\r42%...\r42%...\r42%...\r42%...\r43%...\r43%...\r43%...\r43%...\r43%...\r44%...\r44%...\r44%...\r44%...\r44%...\r45%...\r45%...\r45%...\r45%...\r45%...\r46%...\r46%...\r46%...\r46%...\r46%...\r47%...\r47%...\r47%...\r47%...\r47%...\r48%...\r48%...\r48%...\r48%...\r48%...\r49%...\r49%...\r49%...\r49%...\r49%...\r50%...\r50%...\r50%...\r50%...\r50%...\r51%...\r51%...\r51%...\r51%...\r51%...\r52%...\r52%...\r52%...\r52%...\r52%...\r53%...\r53%...\r53%...\r53%...\r53%...\r54%...\r54%...\r54%...\r54%...\r54%...\r55%...\r55%...\r55%...\r55%...\r55%...\r56%...\r56%...\r56%...\r56%...\r56%...\r57%...\r57%...\r57%...\r57%...\r57%...\r58%...\r58%...\r58%...\r58%...\r58%...\r59%...\r59%...\r59%...\r59%...\r59%...\r60%...\r60%...\r60%...\r60%...\r60%...\r61%...\r61%...\r61%...\r61%...\r61%...\r62%...\r62%...\r62%...\r62%...\r62%...\r63%...\r63%...\r63%...\r63%...\r63%...\r64%...\r64%...\r64%...\r64%...\r64%...\r65%...\r65%...\r65%...\r65%...\r65%...\r66%...\r66%...\r66%...\r66%...\r66%...\r67%...\r67%...\r67%...\r67%...\r67%...\r68%...\r68%...\r68%...\r68%...\r68%...\r69%...\r69%...\r69%...\r69%...\r69%...\r70%...\r70%...\r70%...\r70%...\r70%...\r71%...\r71%...\r71%...\r71%...\r71%...\r72%...\r72%...\r72%...\r72%...\r72%...\r73%...\r73%...\r73%...\r73%...\r73%...\r74%...\r74%...\r74%...\r74%...\r74%...\r75%...\r75%...\r75%...\r75%...\r75%...\r76%...\r76%...\r76%...\r76%...\r76%...\r77%...\r77%...\r77%...\r77%...\r77%...\r78%...\r78%...\r78%...\r78%...\r78%...\r79%...\r79%...\r79%...\r79%...\r79%...\r80%...\r80%...\r80%...\r80%...\r80%...\r81%...\r81%...\r81%...\r81%...\r81%...\r82%...\r82%...\r82%...\r82%...\r82%...\r83%...\r83%...\r83%...\r83%...\r83%...\r84%...\r84%...\r84%...\r84%...\r84%...\r85%...\r85%...\r85%...\r85%...\r85%...\r86%...\r86%...\r86%...\r86%...\r86%...\r87%...\r87%...\r87%...\r87%...\r87%...\r88%...\r88%...\r88%...\r88%...\r88%...\r89%...\r89%...\r89%...\r89%...\r89%...\r90%...\r90%...\r90%...\r90%...\r90%...\r91%...\r91%...\r91%...\r91%...\r91%...\r92%...\r92%...\r92%...\r92%...\r92%...\r93%...\r93%...\r93%...\r93%...\r93%...\r94%...\r94%...\r94%...\r94%...\r94%...\r95%...\r95%...\r95%...\r95%...\r95%...\r96%...\r96%...\r96%...\r96%...\r96%...\r97%...\r97%...\r97%...\r97%...\r97%...\r98%...\r98%...\r98%...\r98%...\r98%...\r99%...\r99%...\r99%...\r99%...\r99%...\n[INFO] Query length 892758.\n[INFO] Writing matrix.\n[INFO] Found 20083 unique hits for z = 4.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "34 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "34.0000000"}, {"title": "Job End Time", "value": "2024-10-05 07:02:59", "plugin": "core", "name": "end_epoch", "raw_value": "1728111779.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 07:02:25", "plugin": "core", "name": "start_epoch", "raw_value": "1728111745.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "datamash_transpose/1.8+galaxy1-0", "has_data": true, "data": {"tool_id": "datamash_transpose", "tool_version": "1.8+galaxy1", "test_index": 0, "time_seconds": 68.73448753356934, "inputs": {"in_file": {"src": "hda", "id": "779d4cab783f0ad5"}}, "job": {"model_class": "Job", "id": "3b88da29b42d9d34", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:26:15.432137", "update_time": "2024-10-05T06:26:56.007295", "galaxy_version": "24.1", "external_id": "gxy-ssh7x", "handler": null, "job_runner_name": null, "command_line": "datamash transpose < /galaxy/server/database/objects/7/d/b/dataset_7dbb9727-7b58-466d-9655-008e23538f17.dat > /galaxy/server/database/objects/8/6/6/dataset_86629209-760a-4d6e-92f8-c5c09a837b73.dat", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"in_file": {"id": "779d4cab783f0ad5", "src": "hda", "uuid": "7dbb9727-7b58-466d-9655-008e23538f17"}}, "outputs": {"out_file": {"id": "3b88da29b42d9d34", "src": "hda", "uuid": "86629209-760a-4d6e-92f8-c5c09a837b73"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:26:43", "plugin": "core", "name": "end_epoch", "raw_value": "1728109603.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:26:43", "plugin": "core", "name": "start_epoch", "raw_value": "1728109603.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_plot_fingerprint/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_plot_fingerprint", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 64.13143706321716, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "1e4681385ecc7453"}, {"src": "hda", "id": "1e4681385ecc7453"}], "advancedOpt|showAdvancedOpt": "no", "output|showOutputSettings": "no"}, "job": {"model_class": "Job", "id": "57809ef5376e1992", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-10-05T06:27:29.567735", "update_time": "2024-10-05T06:28:01.140320", "galaxy_version": "24.1", "external_id": "gxy-dsdtv", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/1/0/4/metadata_104947e0-34a1-43e1-8db9-1cc069aafbe0.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/b/7/9/dataset_b79efeae-155c-4cc8-bbba-283551a339c4.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/1/0/4/metadata_104947e0-34a1-43e1-8db9-1cc069aafbe0.dat' './1.bam.bai' && plotFingerprint --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFile /galaxy/server/database/objects/5/d/3/dataset_5d34d069-292e-4b2d-a397-db6ed9e61c4c.dat --plotFileFormat 'png'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 3, \"src\": \"hda\"}, {\"id\": 3, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibam_conditional|bamfiles2": {"id": "1e4681385ecc7453", "src": "hda", "uuid": "b79efeae-155c-4cc8-bbba-283551a339c4"}, "multibam_conditional|bamfiles1": {"id": "1e4681385ecc7453", "src": "hda", "uuid": "b79efeae-155c-4cc8-bbba-283551a339c4"}, "multibam_conditional|bamfiles": {"id": "1e4681385ecc7453", "src": "hda", "uuid": "b79efeae-155c-4cc8-bbba-283551a339c4"}}, "outputs": {"outFileName": {"id": "57809ef5376e1992", "src": "hda", "uuid": "5d34d069-292e-4b2d-a397-db6ed9e61c4c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "deeptools_plot_fingerprint/3.5.4+galaxy0-1", "has_data": true, "data": {"tool_id": "deeptools_plot_fingerprint", "tool_version": "3.5.4+galaxy0", "test_index": 1, "time_seconds": 23.88559126853943, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-0", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 0, "time_seconds": 43.29050874710083, "inputs": {"alignment": {"src": "hda", "id": "ab25a5964fc57582"}, "anno|reference_gene_sets": {"src": "hda", "id": "4f43e4bab50ab9e8"}, "anno|anno_select": "history", "format": "tabdel_medium", "include_feature_length_file": true}, "job": {"model_class": "Job", "id": "75502bcd39344a71", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:45:57.465943", "update_time": "2024-10-05T06:46:16.576095", "galaxy_version": "24.1", "external_id": "gxy-pfkx9", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/4/d/5/dataset_4d569c1c-180f-4101-9377-2c89a23af474.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > expression_matrix.txt && cut -f 6 body.txt > gene_lengths.txt && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak && mv -f expression_matrix.txt.bak '/galaxy/server/database/objects/c/1/5/dataset_c15fc5f4-ca6d-46a9-a281-eba651b0adc2.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/f/4/1/dataset_f41fef77-9444-46f7-9667-d291348a7939.dat' && sed -e 's|/galaxy/server/database/objects/9/f/d/dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/4/a/e/dataset_4ae0839d-f4e4-4911-95fc-93de9f59667c.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "extended_parameters": "{\"R\": false, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 1, \"count_exon_exon_junction_reads\": \"\"}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "true", "format": "\"tabdel_medium\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 114, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "ab25a5964fc57582", "src": "hda", "uuid": "9fdbd672-5107-4039-b85b-a7c1de8cd95d"}, "anno|reference_gene_sets": {"id": "4f43e4bab50ab9e8", "src": "hda", "uuid": "4d569c1c-180f-4101-9377-2c89a23af474"}}, "outputs": {"output_medium": {"id": "6940f01d49f3eab7", "src": "hda", "uuid": "c15fc5f4-ca6d-46a9-a281-eba651b0adc2"}, "output_summary": {"id": "3bdef6d60132b40e", "src": "hda", "uuid": "4ae0839d-f4e4-4911-95fc-93de9f59667c"}, "output_feature_lengths": {"id": "859c2327b2fb1bbb", "src": "hda", "uuid": "f41fef77-9444-46f7-9667-d291348a7939"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_4d569c1c-180f-4101-9377-2c89a23af474 ... ||\n|| Dir for temp files : ./ ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_4d569c1c-180f-4101-9377-2c89a23af474.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_4d569c1c-180f-4101-9377-2c89a23af474 ... ||\n|| Dir for temp files : ./ ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_4d569c1c-180f-4101-9377-2c89a23af474.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_9fdbd672-5107-4039-b85b-a7c1de8cd95d.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:46:02", "plugin": "core", "name": "end_epoch", "raw_value": "1728110762.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:46:02", "plugin": "core", "name": "start_epoch", "raw_value": "1728110762.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "featurecounts/2.0.3+galaxy2-0", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 0, "time_seconds": 39.19898843765259, "inputs": {"alignment": {"src": "hda", "id": "9bda54e87fae793b"}, "anno|reference_gene_sets": {"src": "hda", "id": "0e9e51d5e353c5ed"}, "anno|anno_select": "history", "format": "tabdel_medium", "include_feature_length_file": true}, "job": {"model_class": "Job", "id": "67075bd0b9719099", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:49:30.694328", "update_time": "2024-10-05T06:49:45.469841", "galaxy_version": "24.1", "external_id": "gxy-tb28m", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/c/e/7/dataset_ce77ae28-4aca-40ef-a60e-83006ca51482.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > expression_matrix.txt && cut -f 6 body.txt > gene_lengths.txt && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak && mv -f expression_matrix.txt.bak '/galaxy/server/database/objects/5/e/4/dataset_5e46e6cb-0335-4e28-8bd8-5bb6c091bc9b.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/6/0/4/dataset_60420d9e-7c27-4816-8e21-c1f28a7c9693.dat' && sed -e 's|/galaxy/server/database/objects/8/0/0/dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/c/a/2/dataset_ca2c6ea1-7497-453a-8536-06373b8549d4.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "extended_parameters": "{\"R\": false, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 1, \"count_exon_exon_junction_reads\": \"\"}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "true", "format": "\"tabdel_medium\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 135, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "9bda54e87fae793b", "src": "hda", "uuid": "8009c056-d820-429f-8b2e-7a9cf35e28ae"}, "anno|reference_gene_sets": {"id": "0e9e51d5e353c5ed", "src": "hda", "uuid": "ce77ae28-4aca-40ef-a60e-83006ca51482"}}, "outputs": {"output_medium": {"id": "6e41773d9f6e8bd7", "src": "hda", "uuid": "5e46e6cb-0335-4e28-8bd8-5bb6c091bc9b"}, "output_summary": {"id": "602ebc097ebb9c60", "src": "hda", "uuid": "ca2c6ea1-7497-453a-8536-06373b8549d4"}, "output_feature_lengths": {"id": "d2a0fb0371b60f8b", "src": "hda", "uuid": "60420d9e-7c27-4816-8e21-c1f28a7c9693"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_ce77ae28-4aca-40ef-a60e-83006ca51482 ... ||\n|| Dir for temp files : ./ ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_ce77ae28-4aca-40ef-a60e-83006ca51482.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_ce77ae28-4aca-40ef-a60e-83006ca51482 ... ||\n|| Dir for temp files : ./ ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_ce77ae28-4aca-40ef-a60e-83006ca51482.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_8009c056-d820-429f-8b2e-7a9cf35e28ae.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:49:32", "plugin": "core", "name": "end_epoch", "raw_value": "1728110972.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:49:32", "plugin": "core", "name": "start_epoch", "raw_value": "1728110972.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "featurecounts/2.0.3+galaxy2-1", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 1, "time_seconds": 23.108651399612427, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-1", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 1, "time_seconds": 39.83343458175659, "inputs": {"alignment": {"src": "hda", "id": "6b6250d123b0f899"}, "anno|reference_gene_sets": {"src": "hda", "id": "87645111b5c153cf"}, "anno|anno_select": "history", "format": "tabdel_full", "include_feature_length_file": true}, "job": {"model_class": "Job", "id": "898527f9e130834e", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:50:09.529266", "update_time": "2024-10-05T06:50:25.146255", "galaxy_version": "24.1", "external_id": "gxy-4bm9g", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/d/6/8/dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat|featureCounts_input1.bam|g' > body.txt && cp body.txt '/galaxy/server/database/objects/5/5/5/dataset_555e8a75-cf5f-4ab4-a2c2-9fd96f79b13a.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/3/4/9/dataset_349325ea-bd0d-4387-8723-817a14ab3c2c.dat' && sed -e 's|/galaxy/server/database/objects/1/1/1/dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/4/2/0/dataset_420d6bb8-9b15-4da7-8aba-54e0a92dd8b9.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "extended_parameters": "{\"R\": false, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 1, \"count_exon_exon_junction_reads\": \"\"}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "true", "format": "\"tabdel_full\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 140, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "6b6250d123b0f899", "src": "hda", "uuid": "11116cef-d215-4fe7-8e6e-987d566fc567"}, "anno|reference_gene_sets": {"id": "87645111b5c153cf", "src": "hda", "uuid": "d689027a-eddb-4607-ba2f-6c984f9cccaf"}}, "outputs": {"output_full": {"id": "bd65503ad7a9af55", "src": "hda", "uuid": "555e8a75-cf5f-4ab4-a2c2-9fd96f79b13a"}, "output_summary": {"id": "0e0dc0e56adbe5f4", "src": "hda", "uuid": "420d6bb8-9b15-4da7-8aba-54e0a92dd8b9"}, "output_feature_lengths": {"id": "6694697af5dcbdcd", "src": "hda", "uuid": "349325ea-bd0d-4387-8723-817a14ab3c2c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_11116cef-d215-4fe7-8e6e-987d566fc567 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf ... ||\n|| Dir for temp files : ./ ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_11116cef-d215-4fe7-8e6e-987d566fc567 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf ... ||\n|| Dir for temp files : ./ ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_d689027a-eddb-4607-ba2f-6c984f9cccaf.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_11116cef-d215-4fe7-8e6e-987d566fc567.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:50:11", "plugin": "core", "name": "end_epoch", "raw_value": "1728111011.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:50:11", "plugin": "core", "name": "start_epoch", "raw_value": "1728111011.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "featurecounts/2.0.3+galaxy2-2", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 2, "time_seconds": 39.79774522781372, "inputs": {"alignment": {"src": "hda", "id": "c3da5b6d7e1b446e"}, "anno|reference_gene_sets": {"src": "hda", "id": "535cbca629a5b5c5"}, "anno|anno_select": "history", "format": "tabdel_short", "include_feature_length_file": true, "extended_parameters|exon_exon_junction_read_counting_enabled|count_exon_exon_junction_reads": "-J"}, "job": {"model_class": "Job", "id": "1fea2b9adc2a0fce", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:47:03.546087", "update_time": "2024-10-05T06:47:19.038693", "galaxy_version": "24.1", "external_id": "gxy-69c67", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/c/0/0/dataset_c00c209c-ba23-4de9-be4f-b3131f056a32.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' -J --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/0/b/e/dataset_0be0c78c-5e01-4d18-adec-2a8f203d15b2.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/d/8/1/dataset_d8140b51-b41f-4eb2-b71b-2aec404a5274.dat' && sed -e 's|/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat|featureCounts_input1.bam|g' 'output.jcounts' > '/galaxy/server/database/objects/9/f/9/dataset_9f90f531-a99b-4748-b642-68cadf49fcc0.dat' && sed -e 's|/galaxy/server/database/objects/6/6/f/dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/c/9/6/dataset_c9604cc7-11a5-4d42-b278-aad5a8b229cf.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "extended_parameters": "{\"R\": false, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 0, \"count_exon_exon_junction_reads\": \"-J\", \"genome\": null}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "true", "format": "\"tabdel_short\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 121, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "c3da5b6d7e1b446e", "src": "hda", "uuid": "66ff471c-d062-4214-867b-33de0c33ffa6"}, "anno|reference_gene_sets": {"id": "535cbca629a5b5c5", "src": "hda", "uuid": "c00c209c-ba23-4de9-be4f-b3131f056a32"}}, "outputs": {"output_short": {"id": "b0417aefeb5a24d9", "src": "hda", "uuid": "0be0c78c-5e01-4d18-adec-2a8f203d15b2"}, "output_summary": {"id": "db1e84f0148fb5d2", "src": "hda", "uuid": "c9604cc7-11a5-4d42-b278-aad5a8b229cf"}, "output_feature_lengths": {"id": "fa49e059f52f6619", "src": "hda", "uuid": "d8140b51-b41f-4eb2-b71b-2aec404a5274"}, "output_jcounts": {"id": "c1e4e0ab9c464d65", "src": "hda", "uuid": "9f90f531-a99b-4748-b642-68cadf49fcc0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_66ff471c-d062-4214-867b-33de0c33ffa6 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_c00c209c-ba23-4de9-be4f-b3131f056a32 ... ||\n|| Dir for temp files : ./ ||\n|| Junction Counting : .jcounts ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_c00c209c-ba23-4de9-be4f-b3131f056a32.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the junction count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_66ff471c-d062-4214-867b-33de0c33ffa6 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_c00c209c-ba23-4de9-be4f-b3131f056a32 ... ||\n|| Dir for temp files : ./ ||\n|| Junction Counting : .jcounts ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_c00c209c-ba23-4de9-be4f-b3131f056a32.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the junction count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:47:05", "plugin": "core", "name": "end_epoch", "raw_value": "1728110825.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:47:05", "plugin": "core", "name": "start_epoch", "raw_value": "1728110825.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "featurecounts/2.0.3+galaxy2-2", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 2, "time_seconds": 39.58640503883362, "inputs": {"alignment": {"src": "hda", "id": "8b790c9bf7dcddba"}, "anno|reference_gene_sets": {"src": "hda", "id": "0f9c4b64c088aaa5"}, "anno|anno_select": "history", "format": "tabdel_short", "include_feature_length_file": true, "extended_parameters|exon_exon_junction_read_counting_enabled|count_exon_exon_junction_reads": "-J"}, "job": {"model_class": "Job", "id": "5117f9fea7c22917", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:50:49.208416", "update_time": "2024-10-05T06:51:04.733981", "galaxy_version": "24.1", "external_id": "gxy-7dtdc", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/4/b/d/dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' -J --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 '/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat|featureCounts_input1.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/2/1/c/dataset_21c1b12d-0965-479d-8dcc-ce8b567bc557.dat' && cut -f 1,6 body.txt > '/galaxy/server/database/objects/e/2/7/dataset_e277f8ed-1eb5-44e3-a4f8-5c88b87b9f4b.dat' && sed -e 's|/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat|featureCounts_input1.bam|g' 'output.jcounts' > '/galaxy/server/database/objects/5/8/a/dataset_58ae8aaf-435f-4432-b313-0f307bfb219e.dat' && sed -e 's|/galaxy/server/database/objects/a/d/a/dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat|featureCounts_input1.bam|g' 'output.summary' > '/galaxy/server/database/objects/b/5/1/dataset_b511b760-4917-4d63-bf70-ed5c6fdcab2b.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "extended_parameters": "{\"R\": false, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 0, \"count_exon_exon_junction_reads\": \"-J\", \"genome\": null}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "true", "format": "\"tabdel_short\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "8b790c9bf7dcddba", "src": "hda", "uuid": "ada6ba16-8fd7-4b8f-964f-c73279cf2dc1"}, "anno|reference_gene_sets": {"id": "0f9c4b64c088aaa5", "src": "hda", "uuid": "4bdcd95d-dd86-41e6-9657-e5b19b8802b2"}}, "outputs": {"output_short": {"id": "9f84c7897e4a143f", "src": "hda", "uuid": "21c1b12d-0965-479d-8dcc-ce8b567bc557"}, "output_summary": {"id": "aeb10c489f7558cc", "src": "hda", "uuid": "b511b760-4917-4d63-bf70-ed5c6fdcab2b"}, "output_feature_lengths": {"id": "39a9f26a41b0fa22", "src": "hda", "uuid": "e277f8ed-1eb5-44e3-a4f8-5c88b87b9f4b"}, "output_jcounts": {"id": "91958e131477903f", "src": "hda", "uuid": "58ae8aaf-435f-4432-b313-0f307bfb219e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2 ... ||\n|| Dir for temp files : ./ ||\n|| Junction Counting : .jcounts ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the junction count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2 ... ||\n|| Dir for temp files : ./ ||\n|| Junction Counting : .jcounts ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2.dat ... ||\n|| Features : 680 ||\n|| Meta-features : 2 ||\n|| Chromosomes/contigs : 1 ||\n|| ||\n|| Process BAM file dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 6236 ||\n|| Successfully assigned alignments : 158 (2.5%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the junction count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:50:51", "plugin": "core", "name": "end_epoch", "raw_value": "1728111051.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:50:51", "plugin": "core", "name": "start_epoch", "raw_value": "1728111051.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "featurecounts/2.0.3+galaxy2-3", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 3, "time_seconds": 22.909834384918213, "inputs": {"alignment": {"src": "hda", "id": "5f4d96ea980a6855"}, "anno|anno_select": "builtin", "format": "tabdel_short", "pe_parameters|paired_end_status": "PE_individual", "extended_parameters|R": true}, "execution_problem": "parameter 'bgenome': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-3", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 3, "time_seconds": 21.800732374191284, "inputs": {"alignment": {"src": "hda", "id": "9ddf4d6c37c686e2"}, "anno|anno_select": "builtin", "format": "tabdel_short", "pe_parameters|paired_end_status": "PE_individual", "extended_parameters|R": true}, "execution_problem": "parameter 'bgenome': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-4", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 4, "time_seconds": 21.081355094909668, "inputs": {"alignment": {"src": "hda", "id": "3f44ab3096ffcc1e"}, "anno|anno_select": "builtin", "format": "tabdel_short", "pe_parameters|paired_end_status": "PE_fragments", "extended_parameters|R": true}, "execution_problem": "parameter 'bgenome': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-4", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 4, "time_seconds": 23.325932264328003, "inputs": {"alignment": {"src": "hda", "id": "a4f48caaf7d6de64"}, "anno|anno_select": "builtin", "format": "tabdel_short", "pe_parameters|paired_end_status": "PE_fragments", "extended_parameters|R": true}, "execution_problem": "parameter 'bgenome': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-5", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 5, "time_seconds": 22.0949764251709, "inputs": {"alignment": {"src": "hda", "id": "eece88bfac2c788c"}, "anno|anno_select": "cached", "format": "tabdel_medium", "include_feature_length_file": true}, "execution_problem": "parameter 'reference_gene_sets_cached': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-5", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 5, "time_seconds": 22.146179676055908, "inputs": {"alignment": {"src": "hda", "id": "75bd376bb51bf5cf"}, "anno|anno_select": "cached", "format": "tabdel_medium", "include_feature_length_file": true}, "execution_problem": "parameter 'reference_gene_sets_cached': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "featurecounts/2.0.3+galaxy2-6", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 6, "time_seconds": 39.6973774433136, "inputs": {"alignment": {"src": "hda", "id": "f638c659a1b65910"}, "anno|reference_gene_sets": {"src": "hda", "id": "26af5c92b2c39c3f"}, "anno|anno_select": "history", "extended_parameters|R": true}, "job": {"model_class": "Job", "id": "9584a994c964fa4e", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:48:50.486237", "update_time": "2024-10-05T06:49:05.135667", "galaxy_version": "24.1", "external_id": "gxy-l8lcb", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/5/0/d/dataset_50de0387-e47c-431d-b148-bcedfa1b1742.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 -R BAM '/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat|subset.sorted.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/3/7/e/dataset_37e3acb7-6871-418f-9c0f-cb8da855a047.dat' && samtools sort --no-PG -o '/galaxy/server/database/objects/2/9/5/dataset_295c8a84-b75c-43d0-a668-eeb0c4fcdc75.dat' -@ ${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" *.featureCounts.bam && sed -e 's|/galaxy/server/database/objects/6/5/e/dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat|subset.sorted.bam|g' 'output.summary' > '/galaxy/server/database/objects/0/d/a/dataset_0da052b4-da72-49ac-9db0-f10b591f53b5.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "extended_parameters": "{\"R\": true, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 1, \"count_exon_exon_junction_reads\": \"\"}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "false", "format": "\"tabdel_short\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 130, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "f638c659a1b65910", "src": "hda", "uuid": "65e9aee4-a631-42ee-9f75-77f7275d7964"}, "anno|reference_gene_sets": {"id": "26af5c92b2c39c3f", "src": "hda", "uuid": "50de0387-e47c-431d-b148-bcedfa1b1742"}}, "outputs": {"output_bam": {"id": "9bb35db4a4a6eb79", "src": "hda", "uuid": "295c8a84-b75c-43d0-a668-eeb0c4fcdc75"}, "output_short": {"id": "ff764b8b794f379f", "src": "hda", "uuid": "37e3acb7-6871-418f-9c0f-cb8da855a047"}, "output_summary": {"id": "31a28c5e839cb4d7", "src": "hda", "uuid": "0da052b4-da72-49ac-9db0-f10b591f53b5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_65e9aee4-a631-42ee-9f75-77f7275d7964 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_50de0387-e47c-431d-b148-bcedfa1b1742 ... ||\n|| Dir for temp files : ./ ||\n|| Assignment details : .featureCounts.bam ||\n|| (Note that files are saved to the output directory) ||\n|| ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_50de0387-e47c-431d-b148-bcedfa1b1742.dat ... ||\n|| Features : 1398 ||\n|| Meta-features : 1389 ||\n|| Chromosomes/contigs : 32 ||\n|| ||\n|| Process BAM file dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 8936 ||\n|| Successfully assigned alignments : 14 (0.2%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n[bam_sort_core] merging from 0 files and 2 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_65e9aee4-a631-42ee-9f75-77f7275d7964 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_50de0387-e47c-431d-b148-bcedfa1b1742 ... ||\n|| Dir for temp files : ./ ||\n|| Assignment details : .featureCounts.bam ||\n|| (Note that files are saved to the output directory) ||\n|| ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_50de0387-e47c-431d-b148-bcedfa1b1742.dat ... ||\n|| Features : 1398 ||\n|| Meta-features : 1389 ||\n|| Chromosomes/contigs : 32 ||\n|| ||\n|| Process BAM file dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 8936 ||\n|| Successfully assigned alignments : 14 (0.2%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n[bam_sort_core] merging from 0 files and 2 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:48:52", "plugin": "core", "name": "end_epoch", "raw_value": "1728110932.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:48:52", "plugin": "core", "name": "start_epoch", "raw_value": "1728110932.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "featurecounts/2.0.3+galaxy2-6", "has_data": true, "data": {"tool_id": "featurecounts", "tool_version": "2.0.3+galaxy2", "test_index": 6, "time_seconds": 39.71912407875061, "inputs": {"alignment": {"src": "hda", "id": "fda5aebbce7c2848"}, "anno|reference_gene_sets": {"src": "hda", "id": "a98703bac41e5fd0"}, "anno|anno_select": "history", "extended_parameters|R": true}, "job": {"model_class": "Job", "id": "ab25a5964fc57582", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:52:37.662522", "update_time": "2024-10-05T06:52:51.897921", "galaxy_version": "24.1", "external_id": "gxy-km77j", "handler": null, "job_runner_name": null, "command_line": "export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && featureCounts -a '/galaxy/server/database/objects/c/6/d/dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83.dat' -F \"GTF\" -o \"output\" -T ${GALAXY_SLOTS:-2} -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0 -R BAM '/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat' && grep -v \"^#\" \"output\" | sed -e 's|/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat|subset.sorted.bam|g' > body.txt && cut -f 1,7 body.txt > '/galaxy/server/database/objects/0/9/1/dataset_091fa6c5-4727-4678-9eeb-23251579ff2e.dat' && samtools sort --no-PG -o '/galaxy/server/database/objects/9/2/3/dataset_9233b959-c356-4abe-ac56-62607905de86.dat' -@ ${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" *.featureCounts.bam && sed -e 's|/galaxy/server/database/objects/c/f/9/dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat|subset.sorted.bam|g' 'output.summary' > '/galaxy/server/database/objects/1/f/b/dataset_1fb806bc-c185-4443-b880-e9f50f36e8e3.dat'", "user_email": "tests@fake.org", "command_version": "featureCounts v2.0.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "extended_parameters": "{\"R\": true, \"by_read_group\": false, \"exon_exon_junction_read_counting_enabled\": {\"__current_case__\": 1, \"count_exon_exon_junction_reads\": \"\"}, \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"largest_overlap\": false, \"long_reads\": false, \"min_overlap\": \"1\", \"multifeatures\": {\"__current_case__\": 0, \"multifeat\": \"\"}, \"read_extension_3p\": \"0\", \"read_extension_5p\": \"0\", \"read_reduction\": \"\"}", "read_filtering_parameters": "{\"ignore_dup\": false, \"mapping_quality\": \"0\", \"primary\": false, \"splitonly\": \"\"}", "pe_parameters": "{\"__current_case__\": 0, \"paired_end_status\": \"single_end\"}", "include_feature_length_file": "false", "format": "\"tabdel_short\"", "anno": "{\"__current_case__\": 2, \"anno_select\": \"history\", \"gff_feature_attribute\": \"gene_id\", \"gff_feature_type\": \"exon\", \"reference_gene_sets\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}]}, \"summarization_level\": false}", "strand_specificity": "\"0\""}, "inputs": {"alignment": {"id": "fda5aebbce7c2848", "src": "hda", "uuid": "cf99364c-cb55-49bc-98fb-263bc5384b55"}, "anno|reference_gene_sets": {"id": "a98703bac41e5fd0", "src": "hda", "uuid": "c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83"}}, "outputs": {"output_bam": {"id": "b6200d2975339489", "src": "hda", "uuid": "9233b959-c356-4abe-ac56-62607905de86"}, "output_short": {"id": "faa5496b14d1cee0", "src": "hda", "uuid": "091fa6c5-4727-4678-9eeb-23251579ff2e"}, "output_summary": {"id": "ab010cea83aef04a", "src": "hda", "uuid": "1fb806bc-c185-4443-b880-e9f50f36e8e3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_cf99364c-cb55-49bc-98fb-263bc5384b55 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83 ... ||\n|| Dir for temp files : ./ ||\n|| Assignment details : .featureCounts.bam ||\n|| (Note that files are saved to the output directory) ||\n|| ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83.dat ... ||\n|| Features : 1398 ||\n|| Meta-features : 1389 ||\n|| Chromosomes/contigs : 32 ||\n|| ||\n|| Process BAM file dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 8936 ||\n|| Successfully assigned alignments : 14 (0.2%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n[bam_sort_core] merging from 0 files and 2 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\n ========== _____ _ _ ____ _____ ______ _____ \n ===== / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n ===== | (___ | | | | |_) | |__) | |__ / \\ | | | |\n ==== \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n ==== ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n ========== |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\n\t v2.0.3\n\n//========================== featureCounts setting ===========================\\\\\n|| ||\n|| Input files : 1 BAM file ||\n|| ||\n|| dataset_cf99364c-cb55-49bc-98fb-263bc5384b55 ... ||\n|| ||\n|| Output file : output ||\n|| Summary : output.summary ||\n|| Paired-end : no ||\n|| Count read pairs : no ||\n|| Annotation : dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83 ... ||\n|| Dir for temp files : ./ ||\n|| Assignment details : .featureCounts.bam ||\n|| (Note that files are saved to the output directory) ||\n|| ||\n|| ||\n|| Threads : 2 ||\n|| Level : meta-feature level ||\n|| Multimapping reads : not counted ||\n|| Multi-overlapping reads : not counted ||\n|| Min overlapping bases : 1 ||\n|| ||\n\\\\============================================================================//\n\n//================================= Running ==================================\\\\\n|| ||\n|| Load annotation file dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83.dat ... ||\n|| Features : 1398 ||\n|| Meta-features : 1389 ||\n|| Chromosomes/contigs : 32 ||\n|| ||\n|| Process BAM file dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat... ||\n|| Single-end reads are included. ||\n|| Total alignments : 8936 ||\n|| Successfully assigned alignments : 14 (0.2%) ||\n|| Running time : 0.00 minutes ||\n|| ||\n|| Write the final count table. ||\n|| Write the read assignment summary. ||\n|| ||\n|| Summary of counting results can be found in file \"output.summary\" ||\n|| ||\n\\\\============================================================================//\n\n[bam_sort_core] merging from 0 files and 2 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 06:52:39", "plugin": "core", "name": "end_epoch", "raw_value": "1728111159.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:52:39", "plugin": "core", "name": "start_epoch", "raw_value": "1728111159.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "ivar_getmasked/1.2.2+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_getmasked", "tool_version": "1.2.2+galaxy0", "test_index": 0, "time_seconds": 45.689428091049194, "inputs": {"filtered_tsv": {"src": "hda", "id": "e5a5770433996d5f"}, "primers_bed": {"src": "hda", "id": "500cc07c7ab0dac4"}, "primers_tsv": {"src": "hda", "id": "f1416e09dffc9512"}}, "job": {"model_class": "Job", "id": "c10d58b0c4a4c37d", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:08:07.629915", "update_time": "2024-10-05T07:08:25.191774", "galaxy_version": "24.1", "external_id": "gxy-zb9nd", "handler": null, "job_runner_name": null, "command_line": "ivar getmasked -i '/galaxy/server/database/objects/3/f/8/dataset_3f8f3e4c-859a-42c9-ad05-b3495f625800.dat' -b '/galaxy/server/database/objects/d/0/3/dataset_d031afb9-109c-4f5f-9a2b-ec8adce2d710.dat' -f '/galaxy/server/database/objects/3/a/1/dataset_3a19bd15-8f50-4631-b1e3-a393cf69da60.dat' -p masked_primers", "user_email": "tests@fake.org", "command_version": "iVar version 1.2.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"filtered_tsv": {"id": "e5a5770433996d5f", "src": "hda", "uuid": "3f8f3e4c-859a-42c9-ad05-b3495f625800"}, "primers_bed": {"id": "500cc07c7ab0dac4", "src": "hda", "uuid": "d031afb9-109c-4f5f-9a2b-ec8adce2d710"}, "primers_tsv": {"id": "f1416e09dffc9512", "src": "hda", "uuid": "3a19bd15-8f50-4631-b1e3-a393cf69da60"}}, "outputs": {"masked": {"id": "b235fe73f41d9797", "src": "hda", "uuid": "644ee5b5-b73b-4b4c-8cca-a061f89f13a6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\n400_18_out_L**\t400_23_out_R\t400_32_out_L\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\n400_18_out_L**\t400_23_out_R\t400_32_out_L\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 07:08:12", "plugin": "core", "name": "end_epoch", "raw_value": "1728112092.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 07:08:12", "plugin": "core", "name": "start_epoch", "raw_value": "1728112092.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_filter/2.1.5+galaxy0-0", "has_data": true, "data": {"tool_id": "lofreq_filter", "tool_version": "2.1.5+galaxy0", "test_index": 0, "time_seconds": 39.922425985336304, "inputs": {"invcf": {"src": "hda", "id": "1b5db29840f2de8f"}, "filter_by_type|qual|snvqual_filter|snvqual_thresh": "38", "filter_by_type|qual|snvqual_filter|snvqual": "min-phred", "filter_by_type|qual|indelqual_filter|indelqual_thresh": "20", "filter_by_type|qual|indelqual_filter|indelqual": "min-phred"}, "job": {"model_class": "Job", "id": "91958e131477903f", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:03:41.750069", "update_time": "2024-10-05T07:04:00.333743", "galaxy_version": "24.1", "external_id": "gxy-nx64m", "handler": null, "job_runner_name": null, "command_line": "lofreq filter -i /galaxy/server/database/objects/a/5/1/dataset_a51e1e99-de95-4116-8713-abffc74aa5f4.dat --no-defaults --verbose -Q 38 -K 20 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "flag_or_drop": "\"\"", "sb": "{\"sb_filter\": {\"__current_case__\": 2, \"sb_alpha\": \"0.001\", \"sb_compound\": true, \"sb_indels\": false, \"sb_mtc\": \"fdr\", \"strand_bias\": \"mtc\"}}", "af": "{\"af_max\": \"0.0\", \"af_min\": \"0.0\"}", "coverage": "{\"cov_max\": \"0\", \"cov_min\": \"10\"}", "filter_by_type": "{\"__current_case__\": 0, \"keep_only\": \"\", \"qual\": {\"indelqual_filter\": {\"__current_case__\": 1, \"indelqual\": \"min-phred\", \"indelqual_thresh\": \"20\"}, \"snvqual_filter\": {\"__current_case__\": 1, \"snvqual\": \"min-phred\", \"snvqual_thresh\": \"38\"}}}"}, "inputs": {"invcf": {"id": "1b5db29840f2de8f", "src": "hda", "uuid": "a51e1e99-de95-4116-8713-abffc74aa5f4"}}, "outputs": {"outvcf": {"id": "e76d6afbded94e0d", "src": "hda", "uuid": "e7923a75-91d5-4ece-b83e-de2131874541"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. 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Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, exit_code: None, stderr: Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, exit_code: None, stderr: Skipping default settings\nAt least one type of multiple testing correction requested. 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reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/d/8/8/dataset_d88f636c-feab-4fa9-bb74-50b75eda92f3.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools view -b -@ $addthreads -t \"$reffai\" '/galaxy/server/database/objects/7/3/d/dataset_73dcba4f-567f-48cc-a717-1fe260b4c91f.dat' | samtools sort -O bam -@ $addthreads -m $addmemory\"M\" -o '/galaxy/server/database/objects/0/3/d/dataset_03db1fa2-8b8a-424d-927d-f347f50c4aca.dat' -T \"${TMPDIR:-.}\"", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"equCab2\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 170, \"src\": \"hda\"}]}}"}, "inputs": {"input": {"id": "4cc136505c02fafd", "src": "hda", "uuid": "73dcba4f-567f-48cc-a717-1fe260b4c91f"}, "addref_cond|ref": {"id": 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{"input_type_cond|input_read1": {"id": "e3b889d4657a05fb", "src": "hda", "uuid": "0a08dbcd-c26e-4967-9a4e-4e671e289539"}, "input_type_cond|input_read2": {"id": "644229f8e32129db", "src": "hda", "uuid": "c8106b22-d925-40a5-874b-8fcba90745f1"}}, "outputs": {"out_log": {"id": "1b92f046e5cab3f6", "src": "hda", "uuid": "e64d4a4a-f1ee-4c47-bcea-45a1eb4d67ac"}, "out": {"id": "e72e27a949e65cd5", "src": "hda", "uuid": "7f9707e1-71cf-45d7-96df-2af1e3d2870d"}, "out2": {"id": "d87d0e2fffaa3f70", "src": "hda", "uuid": "68362aa5-c129-4588-ada7-0bc69bd9b1b5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:33:24", "plugin": "core", "name": "start_epoch", "raw_value": "1728110004.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:33:26", "plugin": "core", "name": "end_epoch", "raw_value": "1728110006.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_extract/1.1.2+galaxy2-1", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 1, "time_seconds": 41.87113380432129, "inputs": {"input_type_cond|input_read1": {"src": "hda", "id": "4ce93ab10a6e1c73"}, "input_type_cond|input_read2": {"src": "hda", "id": "ee358a7876520820"}, "input_type_cond|bc_pattern": "NNNXXX", "input_type_cond|input_type": "paired", "log": true}, "job": {"model_class": "Job", "id": "4480654f925b6a3c", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:37:33.567241", "update_time": "2024-10-05T06:37:50.838531", "galaxy_version": "24.1", "external_id": "gxy-ljw9b", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/d/7/1/dataset_d7146e12-5f11-4fea-acdb-1e2073a44b70.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/2/f/1/dataset_2f1af5da-593d-42fc-9b9b-02c9dd00d6ca.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log='/galaxy/server/database/objects/9/7/6/dataset_97690e6b-dd41-49fa-ad63-ca2865ecc9c6.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/6/7/2/dataset_672dc685-1749-4cd0-b302-469c777296c7.dat' && mv out2.gz '/galaxy/server/database/objects/4/4/d/dataset_44d685b4-b6e3-4f79-bef8-d2db068a1333.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "true", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "error_correct_cell": "false", "blacklist": null, "whitelist": null, "ignore_read_pair_suffixes": "false", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", "input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"NNNXXX\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 66, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}"}, "inputs": {"input_type_cond|input_read1": {"id": "4ce93ab10a6e1c73", "src": "hda", "uuid": "d7146e12-5f11-4fea-acdb-1e2073a44b70"}, "input_type_cond|input_read2": {"id": "ee358a7876520820", "src": "hda", "uuid": "2f1af5da-593d-42fc-9b9b-02c9dd00d6ca"}}, "outputs": {"out": {"id": "025396b06fd9f207", "src": "hda", "uuid": "672dc685-1749-4cd0-b302-469c777296c7"}, "out2": {"id": "d2f410c19987bd26", "src": "hda", "uuid": "44d685b4-b6e3-4f79-bef8-d2db068a1333"}, "out_log": {"id": "5018ff1d4058493c", "src": "hda", "uuid": "97690e6b-dd41-49fa-ad63-ca2865ecc9c6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:37:37", "plugin": "core", "name": "end_epoch", "raw_value": "1728110257.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:37:35", "plugin": "core", "name": "start_epoch", "raw_value": "1728110255.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_extract/1.1.2+galaxy2-2", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 2, "time_seconds": 41.023284912109375, "inputs": {"input_type_cond|input_readpair": {"src": "hdca", "id": "779d4cab783f0ad5"}, "input_type_cond|bc_pattern": "NNNXXX", "input_type_cond|input_type": "paired_collection", "log": true}, "job": {"model_class": "Job", "id": "894592df6446a85c", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:30:23.021942", "update_time": 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[{\"id\": 1, \"src\": \"hdca\"}]}, \"input_type\": \"paired_collection\", \"reconcile_pairs\": false}", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", "ignore_read_pair_suffixes": "false", "whitelist": null, "blacklist": null, "error_correct_cell": "false", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "log": "true", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input_type_cond|input_readpair2": {"id": "13fc19f852e156cc", "src": "hda", "uuid": "9f691063-3e38-4133-82d2-d29c45e6e414"}, "input_type_cond|input_readpair1": {"id": "abdc18f794870e73", "src": "hda", "uuid": "6e627e9d-74b3-4422-8856-e9d2502212ca"}}, "outputs": {"out_paired_collection|__part__|forward": {"id": "5ec7144545af8589", "src": "hda", "uuid": "334eaa00-c2f1-4e99-8562-11ea97e9fd15"}, "out_paired_collection|__part__|reverse": {"id": "29ee25cbd61b509a", "src": "hda", "uuid": "44ad62d0-76dd-448b-9ea9-89fa8a841516"}, "out_log": {"id": "d9efec2f13a62343", "src": "hda", "uuid": "a0bd9382-0e4b-4765-ace6-d97e06ed4593"}}, "copied_from_job_id": null, "output_collections": {"out_paired_collection": {"src": "hdca", "id": "3b88da29b42d9d34"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:30:25", "plugin": "core", "name": "start_epoch", "raw_value": "1728109825.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:30:27", "plugin": "core", "name": "end_epoch", "raw_value": "1728109827.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": 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'/galaxy/server/database/objects/e/8/f/dataset_e8f57275-5a01-49cd-9cf5-111b9a830743.dat' input_read1.txt && ln -s '/galaxy/server/database/objects/c/4/8/dataset_c483f840-7f8d-4fea-82c7-a43c693039e4.dat' input_read2.txt && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.txt --read2-in=input_read2.txt --stdout '/galaxy/server/database/objects/b/e/4/dataset_be474794-4e6b-4f01-a6fa-9a8d42516fb3.dat' --read2-out='/galaxy/server/database/objects/d/6/2/dataset_d62e4a59-50a1-47b4-8d0d-32dab8b24ad7.dat' False --log='/galaxy/server/database/objects/9/4/2/dataset_942322d6-442b-4371-ad9e-5fe5980d351e.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "true", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "error_correct_cell": "false", "blacklist": null, "whitelist": null, "ignore_read_pair_suffixes": "false", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", "input_type_cond": "{\"__current_case__\": 2, \"bc_pattern\": \"NNNXXX\", \"bc_pattern2\": \"\", \"input_readpair\": {\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}, \"input_type\": \"paired_collection\", \"reconcile_pairs\": false}"}, "inputs": {"input_type_cond|input_readpair2": {"id": "e4b55125ba5df844", "src": "hda", "uuid": "c483f840-7f8d-4fea-82c7-a43c693039e4"}, "input_type_cond|input_readpair1": {"id": "34502251f8acb6a5", "src": "hda", "uuid": "e8f57275-5a01-49cd-9cf5-111b9a830743"}}, "outputs": {"out_paired_collection|__part__|forward": {"id": "52ebb49230a9336d", "src": "hda", "uuid": "be474794-4e6b-4f01-a6fa-9a8d42516fb3"}, "out_paired_collection|__part__|reverse": {"id": "5522a3a41dfc9140", "src": "hda", "uuid": "d62e4a59-50a1-47b4-8d0d-32dab8b24ad7"}, "out_log": {"id": "1fee1f4d1ec01669", "src": "hda", "uuid": 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"umi_tools_extract/1.1.2+galaxy2-2", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 2, "time_seconds": 40.284913063049316, "inputs": {"input_type_cond|input_readpair": {"src": "hdca", "id": "fb91bae129b08fde"}, "input_type_cond|bc_pattern": "NNNXXX", "input_type_cond|input_type": "paired_collection", "log": true}, "job": {"model_class": "Job", "id": "d5536ca3b8f0f513", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:38:15.446090", "update_time": "2024-10-05T06:38:31.519298", "galaxy_version": "24.1", "external_id": "gxy-mbhlc", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/6/0/d/dataset_60d6d110-d7a5-400b-8a23-24853588f2a8.dat' input_read1.txt && ln -s '/galaxy/server/database/objects/3/7/b/dataset_37b191af-99dd-4784-ab03-f7cc2d427bc8.dat' input_read2.txt && umi_tools extract --extract-method='string' --bc-pattern='NNNXXX' --stdin=input_read1.txt --read2-in=input_read2.txt --stdout '/galaxy/server/database/objects/1/c/2/dataset_1c26808d-8eda-404b-b3cf-d1fb784a89e3.dat' --read2-out='/galaxy/server/database/objects/7/c/1/dataset_7c1ab5c6-ca32-42b6-9134-837101ed5ada.dat' False --log='/galaxy/server/database/objects/6/f/4/dataset_6f4d1c97-5b9e-4e3b-bae2-70ca4b027418.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "true", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "error_correct_cell": "false", "blacklist": null, "whitelist": null, "ignore_read_pair_suffixes": "false", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": 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"input_type_cond|input_read2": {"id": "d07edbc21b354e8b", "src": "hda", "uuid": "a34386c7-e30f-496f-8ea3-4b355ae8d82c"}, "whitelist": {"id": "2d7776aa9c65c125", "src": "hda", "uuid": "84c11834-1bc3-46e5-8f36-8cc099aa9c88"}}, "outputs": {"out": {"id": "fdadf5367d57b093", "src": "hda", "uuid": "d10e7085-a1d1-455d-a244-3ee68ba05b85"}, "out2": {"id": "7693fd1fe15f87a1", "src": "hda", "uuid": "f2b56f81-4ce6-40c2-b2b7-ddf0c00d1fd5"}, "out_log": {"id": "f75ceb0d2a04a38b", "src": "hda", "uuid": "bfc2c131-0ec6-47fb-9705-f03773615f36"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:35:35", "plugin": "core", "name": "start_epoch", "raw_value": "1728110135.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:35:37", "plugin": "core", "name": "end_epoch", "raw_value": "1728110137.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_extract/1.1.2+galaxy2-4", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 4, "time_seconds": 45.405049085617065, "inputs": {"input_type_cond|input_read1": {"src": "hda", "id": "95d74e7f0ce53721"}, "input_type_cond|input_read2": {"src": "hda", "id": "e15b5fabc0e0db09"}, "input_type_cond|bc_pattern": "^(?P.{6})(?P.{10})", "input_type_cond|input_type": "paired", "extract_method_cond|extract_method": "regex", "whitelist": {"src": "hda", "id": "b31fdeb32a759538"}, "log": true}, "job": {"model_class": "Job", "id": "53f38b9dd2170918", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:39:36.195240", "update_time": "2024-10-05T06:39:53.041171", "galaxy_version": "24.1", "external_id": "gxy-wmrxq", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/6/0/b/dataset_60b8daa2-0b9f-4bc0-9c21-177dbebacf0f.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/8/6/1/dataset_861e12e2-a95d-4d0d-af04-bc675de3c124.dat' input_read2.gz && umi_tools extract --extract-method='regex' --bc-pattern='^(?P.{6})(?P.{10})' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --whitelist='/galaxy/server/database/objects/7/8/3/dataset_783b4809-7fcf-40ca-8280-18d0c49404a2.dat' False --log='/galaxy/server/database/objects/c/a/0/dataset_ca0ac285-a2c4-420c-8de5-37ed82492c6e.dat' --log2stderr && mv out1.gz '/galaxy/server/database/objects/e/d/e/dataset_ede82578-dbc9-4368-9668-d80ca0f68d7a.dat' && mv out2.gz '/galaxy/server/database/objects/9/5/f/dataset_95f04cab-26f0-4c63-85dd-460d9d507578.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "true", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "error_correct_cell": "false", "blacklist": null, "ignore_read_pair_suffixes": "false", "extract_method_cond": "{\"__current_case__\": 1, \"extract_method\": \"regex\", \"filtered_out_bool\": false}", "input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"^(?P.{6})(?P.{10})\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 82, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}"}, "inputs": {"input_type_cond|input_read1": {"id": "95d74e7f0ce53721", "src": "hda", "uuid": "60b8daa2-0b9f-4bc0-9c21-177dbebacf0f"}, "input_type_cond|input_read2": {"id": "e15b5fabc0e0db09", "src": "hda", "uuid": "861e12e2-a95d-4d0d-af04-bc675de3c124"}, "whitelist": {"id": "b31fdeb32a759538", "src": "hda", "uuid": "783b4809-7fcf-40ca-8280-18d0c49404a2"}}, "outputs": {"out": {"id": "066e0eaa4712a55e", "src": "hda", "uuid": "ede82578-dbc9-4368-9668-d80ca0f68d7a"}, "out2": {"id": "06e787421fe23b00", "src": "hda", "uuid": "95f04cab-26f0-4c63-85dd-460d9d507578"}, "out_log": {"id": "a542d32b05dfe07d", "src": "hda", "uuid": "ca0ac285-a2c4-420c-8de5-37ed82492c6e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:39:40", "plugin": "core", "name": "end_epoch", "raw_value": "1728110380.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:39:37", "plugin": "core", "name": "start_epoch", "raw_value": "1728110377.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_extract/1.1.2+galaxy2-5", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 5, "time_seconds": 39.67880845069885, "inputs": {"input_type_cond|input_read1": {"src": "hda", "id": "8f69013b205acde1"}, "input_type_cond|input_read2": {"src": "hda", "id": "2a1b1d1392ee3f4b"}, "input_type_cond|bc_pattern": "NNNNNNCCCCCC", "input_type_cond|input_type": "paired", "extract_method_cond|extract_method": "string"}, "job": {"model_class": "Job", "id": "3cdb8d8f0a4afc83", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:32:00.658868", "update_time": "2024-10-05T06:32:17.485947", "galaxy_version": "24.1", "external_id": "gxy-m6sqb", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/9/c/5/dataset_9c554cb8-32c9-475e-93db-5496c4f245fb.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/b/8/d/dataset_b8d00482-145c-44ac-8530-1a40c4fa5271.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/4/c/f/dataset_4cff3bb0-bf00-482a-8a0c-0fd33cc7578f.dat' && mv out2.gz '/galaxy/server/database/objects/d/5/9/dataset_d5926650-4696-4738-8471-d9ab25977335.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"NNNNNNCCCCCC\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 29, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 30, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", "ignore_read_pair_suffixes": "false", "whitelist": null, "blacklist": null, "error_correct_cell": "false", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input_type_cond|input_read1": {"id": "8f69013b205acde1", "src": "hda", "uuid": "9c554cb8-32c9-475e-93db-5496c4f245fb"}, "input_type_cond|input_read2": {"id": "2a1b1d1392ee3f4b", "src": "hda", "uuid": "b8d00482-145c-44ac-8530-1a40c4fa5271"}}, "outputs": {"out": {"id": "9c4145df767100b6", "src": "hda", "uuid": "4cff3bb0-bf00-482a-8a0c-0fd33cc7578f"}, "out2": {"id": "a0fd35a64b34d145", "src": "hda", "uuid": "d5926650-4696-4738-8471-d9ab25977335"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:32:04 2024 on gxy-m6sqb-b5bhf -- b0d50840-59a4-4cc1-8aad-2330046eaee4\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:32:04,279 INFO Starting barcode extraction\n2024-10-05 06:32:04,287 INFO Input Reads: 50\n2024-10-05 06:32:04,287 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:32:04 2024 -- 1.34 0.26 0.00 0.00 -- b0d50840-59a4-4cc1-8aad-2330046eaee4\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:32:04 2024 on gxy-m6sqb-b5bhf -- b0d50840-59a4-4cc1-8aad-2330046eaee4\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:32:04,279 INFO Starting barcode extraction\n2024-10-05 06:32:04,287 INFO Input Reads: 50\n2024-10-05 06:32:04,287 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:32:04 2024 -- 1.34 0.26 0.00 0.00 -- b0d50840-59a4-4cc1-8aad-2330046eaee4\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:32:02", "plugin": "core", "name": "start_epoch", "raw_value": "1728109922.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:32:04", "plugin": "core", "name": "end_epoch", "raw_value": "1728109924.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_extract/1.1.2+galaxy2-5", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 5, "time_seconds": 39.73489165306091, "inputs": {"input_type_cond|input_read1": {"src": "hda", "id": "a4ef26c5b1d85e43"}, "input_type_cond|input_read2": {"src": "hda", "id": "53f38b9dd2170918"}, "input_type_cond|bc_pattern": "NNNNNNCCCCCC", "input_type_cond|input_type": "paired", "extract_method_cond|extract_method": "string"}, "job": {"model_class": "Job", "id": "52ebb49230a9336d", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T06:36:13.664425", "update_time": "2024-10-05T06:36:29.974148", "galaxy_version": "24.1", "external_id": "gxy-5hdm7", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/d/f/8/dataset_df88a6ab-3eee-4161-9276-425ab70f26d3.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/d/c/d/dataset_dcd26eea-8bb3-4ca7-a47d-2a1e7816c8ca.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/0/5/d/dataset_05ddf729-db3a-49a3-855f-4977775dacab.dat' && mv out2.gz '/galaxy/server/database/objects/6/3/e/dataset_63e9bcca-69e2-48ea-8ae7-9e70360eb30a.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "error_correct_cell": "false", "blacklist": null, "whitelist": null, "ignore_read_pair_suffixes": "false", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", "input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"NNNNNNCCCCCC\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 58, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}"}, "inputs": {"input_type_cond|input_read1": {"id": "a4ef26c5b1d85e43", "src": "hda", "uuid": "df88a6ab-3eee-4161-9276-425ab70f26d3"}, "input_type_cond|input_read2": {"id": "53f38b9dd2170918", "src": "hda", "uuid": "dcd26eea-8bb3-4ca7-a47d-2a1e7816c8ca"}}, "outputs": {"out": {"id": "e8de2f61a615df46", "src": "hda", "uuid": "05ddf729-db3a-49a3-855f-4977775dacab"}, "out2": {"id": "943a976c3b379a43", "src": "hda", "uuid": "63e9bcca-69e2-48ea-8ae7-9e70360eb30a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:36:17 2024 on gxy-5hdm7-wkbc5 -- acd007e2-0e54-479d-9089-401d8d837382\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:36:17,302 INFO Starting barcode extraction\n2024-10-05 06:36:17,310 INFO Input Reads: 50\n2024-10-05 06:36:17,310 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:36:17 2024 -- 1.36 0.26 0.00 0.00 -- acd007e2-0e54-479d-9089-401d8d837382\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:36:17 2024 on gxy-5hdm7-wkbc5 -- acd007e2-0e54-479d-9089-401d8d837382\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:36:17,302 INFO Starting barcode extraction\n2024-10-05 06:36:17,310 INFO Input Reads: 50\n2024-10-05 06:36:17,310 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:36:17 2024 -- 1.36 0.26 0.00 0.00 -- acd007e2-0e54-479d-9089-401d8d837382\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 06:36:15", "plugin": "core", "name": "start_epoch", "raw_value": "1728110175.0000000"}, {"title": "Job End Time", "value": "2024-10-05 06:36:17", "plugin": "core", "name": "end_epoch", "raw_value": "1728110177.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_extract/1.1.2+galaxy2-5", "has_data": true, "data": {"tool_id": "umi_tools_extract", "tool_version": "1.1.2+galaxy2", "test_index": 5, "time_seconds": 30.181332111358643, "inputs": {"input_type_cond|input_read1": {"src": "hda", "id": "75502bcd39344a71"}, "input_type_cond|input_read2": {"src": "hda", "id": "20a79f958a1ad4a1"}, "input_type_cond|bc_pattern": "NNNNNNCCCCCC", "input_type_cond|input_type": "paired", "extract_method_cond|extract_method": "string"}, "job": {"model_class": "Job", "id": "2704ccb375827a9b", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "state": "error", "exit_code": null, "create_time": "2024-10-05T06:40:17.162455", "update_time": "2024-10-05T06:40:23.333336", "galaxy_version": "24.1", "external_id": "gxy-7nbzx", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/9/9/dataset_b99998c9-5079-466a-bd90-6b4ac47ef392.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/e/f/d/dataset_efd26cbf-3208-4678-be8b-be73c00f4356.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/5/1/b/dataset_51bc75bf-3db8-4f22-9b83-0177410c5511.dat' && mv out2.gz '/galaxy/server/database/objects/c/8/5/dataset_c850d4a7-42a1-430b-81e0-4ea7da635e32.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}", "error_correct_cell": "false", "blacklist": null, "whitelist": null, "ignore_read_pair_suffixes": "false", "extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}", "input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"NNNNNNCCCCCC\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 87, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}"}, "inputs": {"input_type_cond|input_read1": {"id": "75502bcd39344a71", "src": "hda", "uuid": "b99998c9-5079-466a-bd90-6b4ac47ef392"}, "input_type_cond|input_read2": {"id": "20a79f958a1ad4a1", "src": "hda", "uuid": "efd26cbf-3208-4678-be8b-be73c00f4356"}}, "outputs": {"out": {"id": "db5a2d4573973b22", "src": "hda", "uuid": "51bc75bf-3db8-4f22-9b83-0177410c5511"}, "out2": {"id": "1901d0f883d04f28", "src": "hda", "uuid": "c850d4a7-42a1-430b-81e0-4ea7da635e32"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, exit_code: None, stderr: # UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, exit_code: None, stderr: # UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, exit_code: None, stderr: # UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n."], "status": "failure"}}, {"id": "vcfannotate/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfannotate", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 13.083466053009033, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "vcfrandomsample/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfrandomsample", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 42.718214988708496, "inputs": {"vcf_input": {"src": "hda", "id": "cd92f0c973d7bbd0"}, "rate": "0.2", "random_seed": "1", "adv_options|adv_options_selector": "no"}, "job": {"model_class": "Job", "id": "2d27de61c475e487", "history_id": "779d4cab783f0ad5", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-10-05T07:07:17.628430", "update_time": "2024-10-05T07:07:38.562664", "galaxy_version": "24.1", "external_id": "gxy-vfhfj", "handler": null, "job_runner_name": null, "command_line": "vcfrandomsample -p 1 -r 0.2 '/galaxy/server/database/objects/1/2/e/dataset_12ee58c3-4bb8-454d-9d2c-18783fff2c6c.dat' > '/galaxy/server/database/objects/3/1/b/dataset_31b88afb-a64c-4f2d-8f32-35225db5c755.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv_options": "{\"__current_case__\": 0, \"adv_options_selector\": \"no\"}", "random_seed": "\"1\"", "rate": "\"0.2\""}, "inputs": {"vcf_input": {"id": "cd92f0c973d7bbd0", "src": "hda", "uuid": "12ee58c3-4bb8-454d-9d2c-18783fff2c6c"}}, "outputs": {"out_file1": {"id": "5c2b08d5380c4d38", "src": "hda", "uuid": "31b88afb-a64c-4f2d-8f32-35225db5c755"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-10-05 07:07:24", "plugin": "core", "name": "end_epoch", "raw_value": "1728112044.0000000"}, {"title": "Job Start Time", "value": "2024-10-05 07:07:24", "plugin": "core", "name": "start_epoch", "raw_value": "1728112044.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}], "galaxy_url": "http://34.139.155.9:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.xunit new file mode 100644 index 000000000..c3e50a422 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.xunit @@ -0,0 +1,824 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .jcounts |||| |||| Threads : 2 |||| Level : meta-feature level |||| Multimapping reads : not counted |||| Multi-overlapping reads : not counted |||| Min overlapping bases : 1 |||| ||\\============================================================================////================================= Running ==================================\\|| |||| Load annotation file dataset_c00c209c-ba23-4de9-be4f-b3131f056a32.dat ... |||| Features : 680 |||| Meta-features : 2 |||| Chromosomes/contigs : 1 |||| |||| Process BAM file dataset_66ff471c-d062-4214-867b-33de0c33ffa6.dat... |||| Single-end reads are included. |||| Total alignments : 6236 |||| Successfully assigned alignments : 158 (2.5%) |||| Running time : 0.00 minutes |||| |||| Write the final count table. |||| Write the junction count table. |||| Write the read assignment summary. |||| |||| Summary of counting results can be found in file "output.summary" |||| ||\\============================================================================// + ]]> + + + + + + + + .jcounts |||| |||| Threads : 2 |||| Level : meta-feature level |||| Multimapping reads : not counted |||| Multi-overlapping reads : not counted |||| Min overlapping bases : 1 |||| ||\\============================================================================////================================= Running ==================================\\|| |||| Load annotation file dataset_4bdcd95d-dd86-41e6-9657-e5b19b8802b2.dat ... |||| Features : 680 |||| Meta-features : 2 |||| Chromosomes/contigs : 1 |||| |||| Process BAM file dataset_ada6ba16-8fd7-4b8f-964f-c73279cf2dc1.dat... |||| Single-end reads are included. |||| Total alignments : 6236 |||| Successfully assigned alignments : 158 (2.5%) |||| Running time : 0.00 minutes |||| |||| Write the final count table. |||| Write the junction count table. |||| Write the read assignment summary. |||| |||| Summary of counting results can be found in file "output.summary" |||| ||\\============================================================================// + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .featureCounts.bam |||| (Note that files are saved to the output directory) |||| |||| |||| Threads : 2 |||| Level : meta-feature level |||| Multimapping reads : not counted |||| Multi-overlapping reads : not counted |||| Min overlapping bases : 1 |||| ||\\============================================================================////================================= Running ==================================\\|| |||| Load annotation file dataset_50de0387-e47c-431d-b148-bcedfa1b1742.dat ... |||| Features : 1398 |||| Meta-features : 1389 |||| Chromosomes/contigs : 32 |||| |||| Process BAM file dataset_65e9aee4-a631-42ee-9f75-77f7275d7964.dat... |||| Single-end reads are included. |||| Total alignments : 8936 |||| Successfully assigned alignments : 14 (0.2%) |||| Running time : 0.00 minutes |||| |||| Write the final count table. |||| Write the read assignment summary. |||| |||| Summary of counting results can be found in file "output.summary" |||| ||\\============================================================================//[bam_sort_core] merging from 0 files and 2 in-memory blocks... + ]]> + + + + + + + + .featureCounts.bam |||| (Note that files are saved to the output directory) |||| |||| |||| Threads : 2 |||| Level : meta-feature level |||| Multimapping reads : not counted |||| Multi-overlapping reads : not counted |||| Min overlapping bases : 1 |||| ||\\============================================================================////================================= Running ==================================\\|| |||| Load annotation file dataset_c6d9595d-dd9c-48cc-a97f-4a1ef16f3f83.dat ... |||| Features : 1398 |||| Meta-features : 1389 |||| Chromosomes/contigs : 32 |||| |||| Process BAM file dataset_cf99364c-cb55-49bc-98fb-263bc5384b55.dat... |||| Single-end reads are included. |||| Total alignments : 8936 |||| Successfully assigned alignments : 14 (0.2%) |||| Running time : 0.00 minutes |||| |||| Write the final count table. |||| Write the read assignment summary. |||| |||| Summary of counting results can be found in file "output.summary" |||| ||\\============================================================================//[bam_sort_core] merging from 0 files and 2 in-memory blocks... + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'># timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_correct_log : None# umi_whitelist : None# umi_whitelist_paired : None# whitelist : None2024-10-05 06:32:04,279 INFO Starting barcode extraction2024-10-05 06:32:04,287 INFO Input Reads: 502024-10-05 06:32:04,287 INFO Reads output: 50# job finished in 0 seconds at Sat Oct 5 06:32:04 2024 -- 1.34 0.26 0.00 0.00 -- b0d50840-59a4-4cc1-8aad-2330046eaee4 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'># timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_correct_log : None# umi_whitelist : None# umi_whitelist_paired : None# whitelist : None2024-10-05 06:36:17,302 INFO Starting barcode extraction2024-10-05 06:36:17,310 INFO Input Reads: 502024-10-05 06:36:17,310 INFO Reads output: 50# job finished in 0 seconds at Sat Oct 5 06:36:17 2024 -- 1.36 0.26 0.00 0.00 -- acd007e2-0e54-479d-9089-401d8d837382 + ]]> + + + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'># timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_correct_log : None# umi_whitelist : None# umi_whitelist_paired : None# whitelist : None2024-10-05 06:40:20,721 INFO Starting barcode extraction2024-10-05 06:40:20,728 INFO Input Reads: 502024-10-05 06:40:20,729 INFO Reads output: 50# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794 + ]]> + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml new file mode 100644 index 000000000..370c73929 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml @@ -0,0 +1,127 @@ +chunk: 10 +tools: +- name: datamash_transpose + owner: iuc + revisions: + - ac092723240d + tool_panel_section_id: datamash + tool_panel_section_label: Datamash +- name: deeptools_plot_fingerprint + owner: bgruening + revisions: + - 2da482e408b8 + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: umi_tools_extract + owner: iuc + revisions: + - 6a675c3aa610 + - 99aea37a7ff7 + - f3759eec3018 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: bwa + owner: devteam + revisions: + - 3fe632431b68 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: medaka_variant_pipeline + owner: iuc + revisions: + - 336b3def9b2b + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: poretools_qualdist + owner: iuc + revisions: + - ae9060e764b5 + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: featurecounts + owner: iuc + revisions: + - 38b6d12edc68 + - f3a5f075498f + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: samtools_fixmate + owner: iuc + revisions: + - bc0cc7bfbfe9 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: sam_to_bam + owner: devteam + revisions: + - cf1ffd88f895 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: chromeister + owner: iuc + revisions: + - e483be1014b6 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: slice_image + owner: imgteam + revisions: + - 8856a7c85e4c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_read_10x + owner: ebi-gxa + revisions: + - c8391a25dee3 + - d92e6f12b790 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_run_tsne + owner: ebi-gxa + revisions: + - 384cacc40611 + - 8eff7ec034e3 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: add_input_name_as_column + owner: mvdbeek + revisions: + - 3284b72eef56 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: lofreq_filter + owner: iuc + revisions: + - 7dfca164d2e3 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_query_list_samples + owner: iuc + revisions: + - ed4ea9de1791 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_isec + owner: iuc + revisions: + - 02f349bdbf96 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfannotate + owner: devteam + revisions: + - 01e0321aca98 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfrandomsample + owner: devteam + revisions: + - 6257ee3b50d3 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: ivar_getmasked + owner: iuc + revisions: + - 2cf4a1cafc16 + tool_panel_section_id: virology + tool_panel_section_label: Virology