diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index 02a2f0663..5b8d8a258 100644 --- a/reports/anvil-production/README.md +++ b/reports/anvil-production/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 09 00:49:24 2024Mon Sep 02 00:49:36 2024
1ToolsetMon Sep 09 12:50:13 2024Mon Sep 02 12:49:25 2024
2ToolsetTue Sep 10 00:48:20 2024Tue Sep 03 00:47:25 2024
3ToolsetTue Sep 10 12:51:55 2024Tue Sep 03 12:49:09 2024
4ToolsetWed Sep 04 00:47:35 2024Wed Aug 28 00:47:17 2024
5ToolsetWed Sep 11 12:50:17 2024Wed Sep 04 12:49:18 2024
6ToolsetThu Sep 12 00:49:13 2024Thu Sep 05 00:47:53 2024
7ToolsetThu Aug 29 12:48:26 2024Thu Aug 22 12:47:28 2024
8ToolsetFri Sep 06 00:47:43 2024Fri Aug 30 00:47:54 2024
9ToolsetFri Sep 06 12:48:21 2024Fri Aug 30 12:48:09 2024
10ToolsetSat Sep 07 00:54:23 2024Sat Aug 31 00:46:38 2024
11ToolsetSat Sep 07 12:45:43 2024Sat Aug 31 12:46:14 2024
12ToolsetSun Sep 08 00:51:47 2024Sun Sep 01 00:54:13 2024
13ToolsetSun Sep 08 12:46:16 2024Sun Sep 01 12:46:15 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 09 00:49:24 2024Mon Sep 02 00:49:36 2024
1ToolsetMon Sep 09 12:50:13 2024Mon Sep 02 12:49:25 2024
2ToolsetTue Sep 10 00:48:20 2024Tue Sep 03 00:47:25 2024
3ToolsetTue Sep 10 12:51:55 2024Tue Sep 03 12:49:09 2024
4ToolsetWed Sep 04 00:47:35 2024Wed Aug 28 00:47:17 2024
5ToolsetWed Sep 11 12:50:17 2024Wed Sep 04 12:49:18 2024
6ToolsetThu Sep 12 00:49:13 2024Thu Sep 05 00:47:53 2024
7ToolsetThu Sep 12 12:49:05 2024Thu Aug 29 12:48:26 2024
8ToolsetFri Sep 06 00:47:43 2024Fri Aug 30 00:47:54 2024
9ToolsetFri Sep 06 12:48:21 2024Fri Aug 30 12:48:09 2024
10ToolsetSat Sep 07 00:54:23 2024Sat Aug 31 00:46:38 2024
11ToolsetSat Sep 07 12:45:43 2024Sat Aug 31 12:46:14 2024
12ToolsetSun Sep 08 00:51:47 2024Sun Sep 01 00:54:13 2024
13ToolsetSun Sep 08 12:46:16 2024Sun Sep 01 12:46:15 2024
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index dd0f773f5..17ed85dfe 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -91,10 +91,10 @@ "date2": "Mon Sep 02 00:49:36 2024" }, "7": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-29-12-33-1/results.html", - "date1": "Thu Aug 29 12:48:26 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-29-12-33-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-22-12-32-1/results.html", - "date2": "Thu Aug 22 12:47:28 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.html", + "date1": "Thu Sep 12 12:49:05 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-29-12-33-1/results.html", + "date2": "Thu Aug 29 12:48:26 2024" } } \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/chunk.json new file mode 100644 index 000000000..45f4d6167 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/chunk.json @@ -0,0 +1,7 @@ +{ + "7": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.html", + "date1": "Thu Sep 12 12:49:05 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/chunk.txt new file mode 100644 index 000000000..07a0e8883 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/chunk.txt @@ -0,0 +1,15 @@ +-t query_tabular --tool-version 83069b38aa85 +-t column_remove_by_header --tool-version 372967836e98 +-t multiqc --tool-version 75c93c70d094 +-t samtools_phase --tool-version b5c3b1856370 +-t samtools_mpileup --tool-version fa7ad9b89f4a +-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 nanoplot --tool-version edbb6c5028f5 +-t poretools_extract --tool-version 7e4f1ed70187 +-t deeptools_plot_fingerprint --tool-version 2da482e408b8 +-t lofreq_call --tool-version e1461b5c52a0 +-t ivar_getmasked --tool-version 2cf4a1cafc16 +-t jbrowse --tool-version 4542035c1075 diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/051dc5929d40d789.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/051dc5929d40d789.json new file mode 100644 index 000000000..0a8a3cd2d --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/051dc5929d40d789.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "051dc5929d40d789", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:17:15.315642", + "create_time": "2024-09-12T13:17:05.462355", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-hrbwr", + "command_line": "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' '191:/galaxy/server/database/objects/7/e/e/dataset_7ee98eb7-428a-4eb2-bbcc-e05132669719_files:/galaxy/server/database/objects/7/e/e/dataset_7ee98eb7-428a-4eb2-bbcc-e05132669719.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_doiva6e1\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"merlin.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_nd_hs997\", \"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": "d7051c304663c861", + "src": "hda", + "uuid": "7ee98eb7-428a-4eb2-bbcc-e05132669719" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/15bdeb011f2c4bbe.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/15bdeb011f2c4bbe.json new file mode 100644 index 000000000..bcc5e8141 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/15bdeb011f2c4bbe.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "15bdeb011f2c4bbe", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T12:53:06.707879", + "create_time": "2024-09-12T12:52:54.843584", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-4xszk", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/29/registry.xml' '/galaxy/server/database/jobs_directory/000/29/upload_params.json' '29:/galaxy/server/database/objects/b/8/6/dataset_b8604271-de17-4052-94c2-32f8b1459355_files:/galaxy/server/database/objects/b/8/6/dataset_b8604271-de17-4052-94c2-32f8b1459355.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_j2n983iw\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bamtools.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_n1f9bpqd\", \"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": "15bdeb011f2c4bbe", + "src": "hda", + "uuid": "b8604271-de17-4052-94c2-32f8b1459355" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/304d24ae36549e7b.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/304d24ae36549e7b.json new file mode 100644 index 000000000..c0f3478d6 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/304d24ae36549e7b.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "304d24ae36549e7b", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T12:52:42.096714", + "create_time": "2024-09-12T12:51:51.807884", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-c68h9", + "command_line": "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' '25:/galaxy/server/database/objects/6/8/a/dataset_68abf4f0-69dc-47eb-88ac-7ad212d0f628_files:/galaxy/server/database/objects/6/8/a/dataset_68abf4f0-69dc-47eb-88ac-7ad212d0f628.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_srwkdmil\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"macs_2.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ju5626ie\", \"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": "304d24ae36549e7b", + "src": "hda", + "uuid": "68abf4f0-69dc-47eb-88ac-7ad212d0f628" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/45fb41c325e9adff.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/45fb41c325e9adff.json new file mode 100644 index 000000000..dfd45c9ce --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/45fb41c325e9adff.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "45fb41c325e9adff", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T12:50:22.032924", + "create_time": "2024-09-12T12:49:41.892176", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-vl57b", + "command_line": "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/f/4/7/dataset_f4769b91-8e52-4976-9b04-2800fe84b398_files:/galaxy/server/database/objects/f/4/7/dataset_f4769b91-8e52-4976-9b04-2800fe84b398.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_w0i8u812\"", + "files_metadata": "{\"__current_case__\": 311, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"in_1.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_a9ksjkx8\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"tabular\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "45fb41c325e9adff", + "src": "hda", + "uuid": "f4769b91-8e52-4976-9b04-2800fe84b398" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/64cd24966d0f4515.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/64cd24966d0f4515.json new file mode 100644 index 000000000..15579ab0f --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/64cd24966d0f4515.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "64cd24966d0f4515", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T12:53:54.554670", + "create_time": "2024-09-12T12:52:59.699426", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-jd4k2", + "command_line": "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' '42:/galaxy/server/database/objects/3/f/6/dataset_3f6a321d-6292-4b4b-8dc6-85e0ecdf72db_files:/galaxy/server/database/objects/3/f/6/dataset_3f6a321d-6292-4b4b-8dc6-85e0ecdf72db.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_pfiahymx\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"picard_collectGcBias.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_v8igl8dk\", \"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": "64cd24966d0f4515", + "src": "hda", + "uuid": "3f6a321d-6292-4b4b-8dc6-85e0ecdf72db" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/7117a621f666bab2.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/7117a621f666bab2.json new file mode 100644 index 000000000..f644b73a6 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/7117a621f666bab2.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "7117a621f666bab2", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T12:54:37.187822", + "create_time": "2024-09-12T12:53:02.841694", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-gfx5m", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/51/registry.xml' '/galaxy/server/database/jobs_directory/000/51/upload_params.json' '51:/galaxy/server/database/objects/a/5/5/dataset_a5546993-87a8-4bda-92db-32150f5074d0_files:/galaxy/server/database/objects/a/5/5/dataset_a5546993-87a8-4bda-92db-32150f5074d0.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_kqsvij5j\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"quast.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_k_39016a\", \"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": "7117a621f666bab2", + "src": "hda", + "uuid": "a5546993-87a8-4bda-92db-32150f5074d0" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/740b63cd736b2680.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/740b63cd736b2680.json new file mode 100644 index 000000000..9b3606098 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/740b63cd736b2680.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "740b63cd736b2680", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:03:24.964889", + "create_time": "2024-09-12T13:03:14.679786", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-pxfkf", + "command_line": "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' '122:/galaxy/server/database/objects/e/2/f/dataset_e2f589c8-f231-492b-b994-306c5617db86_files:/galaxy/server/database/objects/e/2/f/dataset_e2f589c8-f231-492b-b994-306c5617db86.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params__qdknika\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"vcflib.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_r3gxsdn6\", \"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": "fd08b9561a6a74c9", + "src": "hda", + "uuid": "e2f589c8-f231-492b-b994-306c5617db86" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/77906ef2693d8471.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/77906ef2693d8471.json new file mode 100644 index 000000000..22891cf9e --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/77906ef2693d8471.json @@ -0,0 +1,69 @@ +{ + "model_class": "Job", + "id": "77906ef2693d8471", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:06:36.861985", + "create_time": "2024-09-12T13:06:25.039233", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-h46l9", + "command_line": "ln -s '/galaxy/server/database/objects/9/a/1/dataset_9a140251-4c09-4678-ab00-95f3d6a2785c.dat' './read_0.fasta' && ln -s '/galaxy/server/database/objects/d/a/d/dataset_dad0eec8-6d14-484e-a2f4-b6b7adaff47a.dat' './read_1.fasta' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --fasta read_0.fasta read_1.fasta -o '.' && >&2 cat *log", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "customization": "{\"N50\": false, \"color\": null, \"plots\": null}", + "filter": "{\"alength\": false, \"barcoded\": false, \"downsample\": \"\", \"drop_outliers\": false, \"loglength\": false, \"maxlength\": \"\", \"minlength\": \"\", \"minqual\": \"\", \"no_supplementary\": false, \"percentqual\": false, \"readtype\": null, \"runtime_until\": \"\"}", + "mode": "{\"__current_case__\": 1, \"choice\": \"combined\", \"reads\": {\"__current_case__\": 1, \"files\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}, {\"id\": 135, \"src\": \"hda\"}]}, \"type\": \"fasta\"}}" + }, + "inputs": { + "mode|reads|files": { + "id": "98e036e4ea2088a4", + "src": "hda", + "uuid": "9a140251-4c09-4678-ab00-95f3d6a2785c" + }, + "mode|reads|files1": { + "id": "98e036e4ea2088a4", + "src": "hda", + "uuid": "9a140251-4c09-4678-ab00-95f3d6a2785c" + }, + "mode|reads|files2": { + "id": "24cfce1dc6c71df2", + "src": "hda", + "uuid": "dad0eec8-6d14-484e-a2f4-b6b7adaff47a" + } + }, + "outputs": { + "output_html": { + "id": "12a3dc4644eabc47", + "src": "hda", + "uuid": "da732326-5805-42c6-a2cb-56bd79b0dd07" + }, + "nanostats": { + "id": "e130bbdb3c861c75", + "src": "hda", + "uuid": "cb9405ee-7eed-4979-b09c-0e37a1226c5a" + }, + "nanostats_post_filtering": { + "id": "4233d6fecc29bcb4", + "src": "hda", + "uuid": "b1cb4b85-585a-4e27-88f5-85c3b5862441" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/bde1698b9e2a4825.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/bde1698b9e2a4825.json new file mode 100644 index 000000000..c957990c6 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/bde1698b9e2a4825.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "bde1698b9e2a4825", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:00:17.182571", + "create_time": "2024-09-12T13:00:07.097330", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-qfk66", + "command_line": "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' '107:/galaxy/server/database/objects/e/8/d/dataset_e8dfa894-f835-4854-96ab-f3a83b09494d_files:/galaxy/server/database/objects/e/8/d/dataset_e8dfa894-f835-4854-96ab-f3a83b09494d.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_9j606cyu\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"phiX.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_lvop4pyt\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fasta\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "ff6e2b9c7b9ced76", + "src": "hda", + "uuid": "e8dfa894-f835-4854-96ab-f3a83b09494d" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/c18cd423ba921e33.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/c18cd423ba921e33.json new file mode 100644 index 000000000..2ec5db530 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/c18cd423ba921e33.json @@ -0,0 +1,54 @@ +{ + "model_class": "Job", + "id": "c18cd423ba921e33", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:19:34.271477", + "create_time": "2024-09-12T13:19:28.591671", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-4grm7", + "command_line": "mkdir -p /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files && cp /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 && cp /galaxy/server/database/jobs_directory/000/168/configs/tmpe_v1eztl /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat; cp /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat", + "traceback": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "uglyTestingHack": "\"enabled\"", + "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", + "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", + "track_groups": "[{\"__index__\": 0, \"category\": \"External endpoints\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 5, \"data_format_select\": \"rest\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Rest api\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/rest_api/\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 6, \"data_format_select\": \"sparql\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Sparql endpoint\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"query\": \" DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/sparql/\"}}]}]", + "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", + "gencode": "\"11\"", + "standalone": "\"data\"", + "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 197, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" + }, + "inputs": { + "reference_genome|genome": { + "id": "e86b9dfb6d985c8c", + "src": "hda", + "uuid": "2ed33cef-cd23-4e80-84be-8480e7ce1da5" + } + }, + "outputs": { + "output": { + "id": "a5948005d8a94f42", + "src": "hda", + "uuid": "4732c9b8-5134-40db-93aa-e15a5b2e43b4" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/e1cfa608ff6717f3.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/e1cfa608ff6717f3.json new file mode 100644 index 000000000..7b07305f5 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/e1cfa608ff6717f3.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "e1cfa608ff6717f3", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T12:51:33.997577", + "create_time": "2024-09-12T12:51:22.949406", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-8nlqk", + "command_line": "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/0/0/f/dataset_00fe3e1e-b737-4f43-baf1-f6e3e3cff424_files:/galaxy/server/database/objects/0/0/f/dataset_00fe3e1e-b737-4f43-baf1-f6e3e3cff424.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_kz5vj5za\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"fastp1.json.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_goykbwka\", \"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": "e1cfa608ff6717f3", + "src": "hda", + "uuid": "00fe3e1e-b737-4f43-baf1-f6e3e3cff424" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/e6d2b9fbd0c20be3.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/e6d2b9fbd0c20be3.json new file mode 100644 index 000000000..3fb55dfad --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/e6d2b9fbd0c20be3.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "e6d2b9fbd0c20be3", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:14:59.814455", + "create_time": "2024-09-12T13:14:49.526405", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-kphl5", + "command_line": "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' '173:/galaxy/server/database/objects/e/0/d/dataset_e0d7f460-5be5-47f2-82b6-3f73259283fe_files:/galaxy/server/database/objects/e/0/d/dataset_e0d7f460-5be5-47f2-82b6-3f73259283fe.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_9xtf9o3s\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"merlin.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_96nkdoq5\", \"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": "0e00f29516f5aa33", + "src": "hda", + "uuid": "e0d7f460-5be5-47f2-82b6-3f73259283fe" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/f981cf37215e9a69.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/f981cf37215e9a69.json new file mode 100644 index 000000000..4e6792f31 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/errors/f981cf37215e9a69.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "f981cf37215e9a69", + "state": "error", + "exit_code": null, + "update_time": "2024-09-12T13:06:49.067855", + "create_time": "2024-09-12T13:06:38.846717", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "45fb41c325e9adff", + "external_id": "gxy-95rb2", + "command_line": "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' '139:/galaxy/server/database/objects/7/9/8/dataset_7981659c-c0f5-4386-99aa-40c089d3fdc5_files:/galaxy/server/database/objects/7/9/8/dataset_7981659c-c0f5-4386-99aa-40c089d3fdc5.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_cse8youy\"", + "files_metadata": "{\"__current_case__\": 240, \"file_type\": \"fast5.tar\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"poretools-in1.tar.bz2\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_c8mulbik\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fast5.tar\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "11d465ee0edd0d83", + "src": "hda", + "uuid": "7981659c-c0f5-4386-99aa-40c089d3fdc5" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/job-metrics.csv b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/job-metrics.csv new file mode 100644 index 000000000..1d77b4f60 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/job-metrics.csv @@ -0,0 +1,169 @@ 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+61b2ac79367bf1c8,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +436c5a64dec43345,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +57c182ccb96215d8,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +d78c1786f6b120c4,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +197618b859a009a4,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +d1bda198af0d517a,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +59987c93d92e9387,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +f56443e0232e3163,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +e81ed87bd4b3bb9f,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +f903a74bd0095a8d,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +c0b5e374a12878e4,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +0781e21f5ef1ae2e,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +64cd24966d0f4515,45fb41c325e9adff,anvil-test-2024-09-12-12-49,error,upload1,,,,,,,,,,, +39cd12fd1ab0057d,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +607573991ddeeb57,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +c7ed71145f28e26b,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +ef34511b8b7ae5ba,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +739ca853df605898,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +f621dfaae50f16a1,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +01a530a9ec9730ed,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +048e88aa913bbcda,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +c90fd3847424484a,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +15bdeb011f2c4bbe,45fb41c325e9adff,anvil-test-2024-09-12-12-49,error,upload1,,,,,,,,,,, +5f532feac224502b,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +4e033c938ee60d15,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +55a99cc289801cf7,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +59943045cd07872d,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +2dc4cf900f397378,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +47e5814df85f2eee,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +304d24ae36549e7b,45fb41c325e9adff,anvil-test-2024-09-12-12-49,error,upload1,,,,,,,,,,, +9ed4d3c53eba5f39,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +d01a421d7a419726,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,8.0000000 +bea69ce4597ec9c3,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,8.0000000 +3bb05cde4086bfcc,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +7b685e9a33fc92d0,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +dc18c08f30cead84,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +9baa567bb6400f27,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,7.0000000 +e45fd8909b026779,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +ec1f1b2fd01b52d9,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +861c9e4011c44858,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +ccf878e22e924f8d,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +8aee079dc1207c82,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +40b6d5d8d35026af,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +21463b5f15f57095,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +7be725bdc42914a2,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +987935bc9fe4a326,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +15321802dc1bada9,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +e1cfa608ff6717f3,45fb41c325e9adff,anvil-test-2024-09-12-12-49,error,upload1,,,,,,,,,,, +2b9702019bfaa3f8,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,column_remove_by_header/1.0,,,,4080.0000000,1.0000000,,,,,,1.0000000 +d51e0424dc6ec33a,45fb41c325e9adff,anvil-test-2024-09-12-12-49,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +45fb41c325e9adff,45fb41c325e9adff,anvil-test-2024-09-12-12-49,error,upload1,,,,,,,,,,, diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/job.log b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/job.log new file mode 100644 index 000000000..9a8cc5403 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/job.log @@ -0,0 +1,18004 @@ +DEBUG:yacman.yacman:Patching yaml loader +DEBUG:galaxy.app:python path is: /galaxy/server/scripts, /galaxy/server/lib, /galaxy/server/lib, /usr/local/lib/python310.zip, /usr/local/lib/python3.10, /usr/local/lib/python3.10/lib-dynload, /galaxy/server/.venv/lib/python3.10/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. +DEBUG:galaxy.web_stack:WeblessApplicationStack initialized +DEBUG:galaxy.web_stack:Will attach to pool(s): job-handlers +galaxy.jobs DEBUG 2024-09-12 12:47:09,555 [pN:job_handler_0,p:9,tN:MainThread] Read job configuration from file: /galaxy/server/config/job_conf.yml +galaxy.jobs INFO 2024-09-12 12:47:09,555 [pN:job_handler_0,p:9,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2024-09-12 12:47:09,555 [pN:job_handler_0,p:9,tN:MainThread] Tag [_default_] handlers: job_handler_0 +galaxy.web_stack.handlers DEBUG 2024-09-12 12:47:09,555 [pN:job_handler_0,p:9,tN:MainThread] default set to child with id or tag 'tpv_dispatcher' +galaxy.jobs DEBUG 2024-09-12 12:47:09,555 [pN:job_handler_0,p:9,tN:MainThread] Done loading job configuration +galaxy.security.vault WARNING 2024-09-12 12:47:09,921 [pN:job_handler_0,p:9,tN:MainThread] No vault configured. We recommend defining the vault_config_file setting in galaxy.yml +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,974 [pN:job_handler_0,p:9,tN:MainThread] Loading datatypes from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,975 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,975 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,975 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,975 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,975 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,976 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,976 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,976 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,976 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,976 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,977 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,978 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,979 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,979 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,979 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,979 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,980 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,981 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,982 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,983 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,983 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,983 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,983 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,983 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,983 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,984 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,985 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,985 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,985 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,985 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,985 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,986 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension data_manager_json. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,987 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,987 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,987 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,987 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,987 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,987 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,988 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,988 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,988 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,988 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,988 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,988 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,989 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,990 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:09,991 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,096 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,097 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,098 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,099 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,100 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,101 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,101 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,101 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,101 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,102 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,102 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,102 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,102 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,102 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,103 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,103 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,103 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,103 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,105 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,105 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,106 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,107 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,108 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,109 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,110 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,111 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,112 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,113 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,114 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,114 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,114 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,114 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,114 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,114 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,115 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,116 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,116 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,116 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,117 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,118 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,118 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,118 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,119 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,119 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,119 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,119 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,120 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,121 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,122 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,123 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,124 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,125 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,126 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,126 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,126 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,126 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,126 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,126 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,127 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,127 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,127 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,127 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,127 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,127 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,128 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,129 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,129 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,129 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,129 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,129 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,129 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,130 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,130 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,130 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,132 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,135 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,136 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,136 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,136 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,136 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,136 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,136 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,137 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,137 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,137 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,137 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,137 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,137 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,138 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,140 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,140 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,141 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,142 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,143 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,144 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,145 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,146 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,146 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,146 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,146 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,146 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,146 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,147 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,148 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,148 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,148 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,148 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,148 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,148 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,149 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,150 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,151 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,152 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,152 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,152 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,152 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,152 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,152 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,153 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,153 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,153 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,153 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,153 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,154 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,154 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,154 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,154 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,154 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,156 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,157 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,157 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,157 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,157 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,157 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,157 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,158 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,158 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,158 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,158 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,159 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,160 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,160 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,160 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,160 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,160 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,160 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,161 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,163 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,164 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,165 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,166 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,167 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,168 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,169 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,169 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,169 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,169 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,169 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,170 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,170 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,170 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,170 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,170 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,171 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,172 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,173 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,174 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,174 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,174 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,174 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,174 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,174 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,175 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,175 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,175 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,175 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,175 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,176 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,176 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,176 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,177 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,177 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,178 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,178 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,178 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,178 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,178 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,179 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,179 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,179 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,179 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,180 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,180 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,180 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,181 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,181 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,181 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,181 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,181 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,182 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,182 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,182 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,182 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,182 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,182 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,183 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,183 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,183 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,184 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,184 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,184 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,184 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,184 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,185 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,185 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,192 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,192 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,192 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,193 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,193 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,193 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,193 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,194 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,194 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,194 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,194 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,194 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,194 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,195 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,195 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,195 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,195 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,195 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,195 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,196 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,197 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,198 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,198 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,198 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,198 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,199 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,201 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,202 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,203 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,204 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,205 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,206 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,207 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,208 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,475 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,476 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,477 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,478 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,479 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,480 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,481 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,482 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,483 [pN:job_handler_0,p:9,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,487 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,488 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,488 [pN:job_handler_0,p:9,tN:MainThread] Loaded build site 'ensembl': /galaxy/server/tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,488 [pN:job_handler_0,p:9,tN:MainThread] Loaded build site 'ensembl_data_url': /galaxy/server/tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,488 [pN:job_handler_0,p:9,tN:MainThread] Loaded build site 'igv': /galaxy/server/tool-data/shared/igv/igv_build_sites.txt.sample +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:10,488 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,489 [pN:job_handler_0,p:9,tN:MainThread] Loading references to tool sheds from internal default config +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-09-12 12:47:10,489 [pN:job_handler_0,p:9,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed +galaxy.web_stack DEBUG 2024-09-12 12:47:10,490 [pN:job_handler_0,p:9,tN:MainThread] server_name set to: job_handler_0 +galaxy.queue_worker INFO 2024-09-12 12:47:10,494 [pN:job_handler_0,p:9,tN:MainThread] Initializing job_handler_0 Galaxy Queue Worker on amqp://default_user_c8xp_WqXtElZ2WQ4Hz1:********@prod-24-09-12-12-33-1-galaxy-rabbitmq-server:5672 +galaxy.tool_util.data WARNING 2024-09-12 12:47:10,516 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,516 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,516 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,517 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,522 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,523 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,525 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,528 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,529 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,530 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,532 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,533 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,534 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,537 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,538 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,541 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,544 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,545 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,549 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,551 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,554 [pN:job_handler_0,p:9,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta_dbkeys.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,555 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,555 [pN:job_handler_0,p:9,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,556 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,556 [pN:job_handler_0,p:9,tN:MainThread] Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,556 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,557 [pN:job_handler_0,p:9,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/alignseq.loc' for 'alignseq_seq' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,557 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,558 [pN:job_handler_0,p:9,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,558 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,559 [pN:job_handler_0,p:9,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,559 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,560 [pN:job_handler_0,p:9,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,560 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,561 [pN:job_handler_0,p:9,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/tophat2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,562 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,562 [pN:job_handler_0,p:9,tN:MainThread] Loaded 59 lines from '/cvmfs/data.galaxyproject.org/managed/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,562 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,563 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,564 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,564 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,564 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,565 [pN:job_handler_0,p:9,tN:MainThread] Loaded 20 lines from '/cvmfs/data.galaxyproject.org/managed/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,565 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,566 [pN:job_handler_0,p:9,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,566 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,567 [pN:job_handler_0,p:9,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken_databases.loc' for 'kraken_databases' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,567 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,568 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,568 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,572 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1193 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys_ucsc.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,572 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,602 [pN:job_handler_0,p:9,tN:MainThread] Loaded 14 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc' for 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,603 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,604 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,604 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,605 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/maf_indexes.loc' for 'maf_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,605 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,606 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,606 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,607 [pN:job_handler_0,p:9,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken2_databases.loc' for 'kraken2_databases' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,607 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,610 [pN:job_handler_0,p:9,tN:MainThread] Loaded 237 lines from '/cvmfs/data.galaxyproject.org/byhand/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,610 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,611 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,612 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,613 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,614 [pN:job_handler_0,p:9,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bfast_indexes.loc' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,614 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,615 [pN:job_handler_0,p:9,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb.loc' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,615 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,616 [pN:job_handler_0,p:9,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb_p.loc' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,616 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,617 [pN:job_handler_0,p:9,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,617 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,619 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,619 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,621 [pN:job_handler_0,p:9,tN:MainThread] Loaded 201 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index.loc' for 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,621 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,622 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,622 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,623 [pN:job_handler_0,p:9,tN:MainThread] Loaded 24 lines from '/cvmfs/data.galaxyproject.org/byhand/location/maf_index.loc' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,624 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,624 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,624 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,625 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,625 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,626 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,626 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,628 [pN:job_handler_0,p:9,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,628 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,630 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,630 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,630 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,630 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,631 [pN:job_handler_0,p:9,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,631 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,634 [pN:job_handler_0,p:9,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'tophat_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,634 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,636 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,636 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,637 [pN:job_handler_0,p:9,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,638 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,639 [pN:job_handler_0,p:9,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ccat_configurations.loc' for 'ccat_configurations' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,640 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,641 [pN:job_handler_0,p:9,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mosaik_index.loc' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,641 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,643 [pN:job_handler_0,p:9,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'bowtie_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,643 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,644 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,644 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,645 [pN:job_handler_0,p:9,tN:MainThread] Loaded 192 lines from '/cvmfs/data.galaxyproject.org/byhand/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,646 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,648 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,649 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,652 [pN:job_handler_0,p:9,tN:MainThread] Loaded 177 lines from '/cvmfs/data.galaxyproject.org/byhand/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,652 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,657 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1181 lines from '/cvmfs/data.galaxyproject.org/byhand/location/liftOver.loc' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,657 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,659 [pN:job_handler_0,p:9,tN:MainThread] Loaded 25 lines from '/cvmfs/data.galaxyproject.org/byhand/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,659 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,660 [pN:job_handler_0,p:9,tN:MainThread] Loaded 106 lines from '/cvmfs/data.galaxyproject.org/byhand/location/customProDB.loc' for 'customProDB' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,660 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,661 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,661 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,662 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,662 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,663 [pN:job_handler_0,p:9,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/snpeffv_genomedb.loc' for 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,663 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,664 [pN:job_handler_0,p:9,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwameth_indexes.loc' for 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,664 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,665 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,665 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,666 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/busco_database.loc' for 'busco_database' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,666 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,667 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,667 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,668 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,668 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,669 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,669 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,670 [pN:job_handler_0,p:9,tN:MainThread] Loaded 8 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rRNA_databases.loc' for 'rRNA_databases' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,670 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,671 [pN:job_handler_0,p:9,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mitos.loc' for 'mitos' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,671 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,672 [pN:job_handler_0,p:9,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_species.loc' for 'dada2_species' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,672 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,673 [pN:job_handler_0,p:9,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_taxonomy.loc' for 'dada2_taxonomy' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,673 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,674 [pN:job_handler_0,p:9,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mapseq_db.loc' for 'mapseq_db' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,674 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,674 [pN:job_handler_0,p:9,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bracken_databases.loc' for 'bracken_databases' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,675 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,675 [pN:job_handler_0,p:9,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/plasmidfinder_database.loc' for 'plasmidfinder_database' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,675 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,676 [pN:job_handler_0,p:9,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus.loc' for 'amrfinderplus_database' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,676 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,677 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus_versioned.loc' for 'amrfinderplus_versioned_database' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,677 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,678 [pN:job_handler_0,p:9,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bakta_database.loc' for 'bakta_database' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,678 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,678 [pN:job_handler_0,p:9,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,679 [pN:job_handler_0,p:9,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 INFO 2024-09-12 12:47:10,680 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/all_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,681 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/all_fasta.loc.sample' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,681 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,681 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bfast_indexes.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,682 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,682 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,682 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,682 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,683 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb.loc.sample' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,683 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,683 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,683 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_p.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,684 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_p.loc.sample' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,684 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,684 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,684 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_d.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,685 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_d.loc.sample' for 'blastdb_d' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,685 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,685 [pN:job_handler_0,p:9,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,685 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,685 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,686 [pN:job_handler_0,p:9,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,686 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,686 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,686 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/maf_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,687 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/maf_index.loc.sample' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,687 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,687 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,688 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,688 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,688 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,689 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_base_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,690 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,690 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,690 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,690 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_color_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,691 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,691 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,691 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,691 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,692 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,692 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,692 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,693 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,693 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,693 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,693 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,694 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/mosaik_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,695 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,695 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,695 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,695 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/twobit.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,696 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/twobit.loc.sample' for 'twobit' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,696 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,696 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,830 [pN:job_handler_0,p:9,tN:MainThread] Encoding detection: utf_8 is most likely the one. +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,830 [pN:job_handler_0,p:9,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-dtz0h5h0". +galaxy.tool_util.data WARNING 2024-09-12 12:47:10,835 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,836 [pN:job_handler_0,p:9,tN:MainThread] Line 2 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): +AccessDeniedAccess Denied1YXKY91MW0B15Y4A3crLhmUqS3a1JbbG5FmCxsTIEXBpCbzzB9890gLJoV+atKIfTZNtKQdwfp8L/tCRgH8RpNEveP4= +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,836 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-dtz0h5h0' for 'igv_broad_genomes' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,837 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,838 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/liftOver.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,839 [pN:job_handler_0,p:9,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/liftOver.loc.sample' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,839 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,839 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,840 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bam_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,841 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/bam_iobio.loc.sample' for 'bam_iobio' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,841 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,841 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/vcf_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,842 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,842 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,842 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/biom_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,843 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,843 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,843 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/intermine_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,844 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,844 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,844 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/icn3d_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,845 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,845 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,845 [pN:job_handler_0,p:9,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,845 [pN:job_handler_0,p:9,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,845 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,845 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,847 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,848 [pN:job_handler_0,p:9,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/q2view_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,848 [pN:job_handler_0,p:9,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/q2view_display.loc.sample' for 'q2view_display' +galaxy.tool_util.data DEBUG 2024-09-12 12:47:10,849 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool data table 'q2view_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.util.dbkeys ERROR 2024-09-12 12:47:10,849 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,964 [pN:job_handler_0,p:9,tN:MainThread] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-09-12 12:47:10,972 [pN:job_handler_0,p:9,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 2024-09-12 12:47:10,972 [pN:job_handler_0,p:9,tN:MainThread] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:10,972 [pN:job_handler_0,p:9,tN:MainThread] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-09-12 12:47:11,021 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,021 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,181 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,181 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,183 [pN:job_handler_0,p:9,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 865, 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 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, 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 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, 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 2024-09-12 12:47:11,218 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,218 [pN:job_handler_0,p:9,tN:MainThread] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:11,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,242 [pN:job_handler_0,p:9,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. +sqlitedict DEBUG 2024-09-12 12:47:11,243 [pN:job_handler_0,p:9,tN:MainThread] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.tool_util.toolbox.base WARNING 2024-09-12 12:47:11,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,319 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,333 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,341 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,349 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,370 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,430 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,438 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,447 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,458 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,466 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,474 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,482 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,489 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,498 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,510 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,519 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,535 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,543 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,550 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,558 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,567 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,574 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,578 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,583 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,588 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,593 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,599 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,604 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,609 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,613 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,618 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,623 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,628 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,633 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,637 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,642 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,647 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,652 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,657 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,661 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,667 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,672 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,676 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,682 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,687 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,692 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,696 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,701 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,709 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,716 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,722 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,729 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,739 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,744 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,752 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,761 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,769 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,775 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,787 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,795 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,802 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,811 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,818 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,824 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,834 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,841 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,850 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,858 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,865 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,873 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,883 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,893 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,903 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,911 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,920 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,927 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,936 [pN:job_handler_0,p:9,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 2024-09-12 12:47:11,944 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,509 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,514 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,527 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,536 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,558 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,569 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,578 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,588 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,596 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,603 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,611 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,618 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,626 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,633 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,641 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,650 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,659 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,667 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,674 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,683 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,692 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,702 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,712 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,720 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,728 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,735 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,743 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,750 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,759 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,766 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,774 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,782 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,791 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,798 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,804 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,812 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,821 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,836 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,853 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,862 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,878 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,883 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,896 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,911 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,924 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,937 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,948 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,953 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,973 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,983 [pN:job_handler_0,p:9,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 2024-09-12 12:47:12,989 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,008 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,016 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,036 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,056 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,064 [pN:job_handler_0,p:9,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. +galaxy.tool_util.toolbox.base WARNING 2024-09-12 12:47:13,098 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,183 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,203 [pN:job_handler_0,p:9,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-09-12 12:47:13,214 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,220 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,243 [pN:job_handler_0,p:9,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-09-12 12:47:13,254 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,295 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,323 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,345 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,350 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,366 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,424 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,444 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,455 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,472 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,494 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,500 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,540 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,563 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,584 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,607 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,614 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,621 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,626 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,633 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,641 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,646 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,656 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,663 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,670 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,676 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,683 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,689 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,696 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,703 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,710 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,719 [pN:job_handler_0,p:9,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 2024-09-12 12:47:13,726 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,000 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,006 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,012 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,017 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,023 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,029 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,034 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,041 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,046 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,051 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,056 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,061 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,066 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,070 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,075 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,081 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,088 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,094 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,101 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,108 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,130 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,181 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,188 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,206 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,219 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,228 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,318 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,325 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,334 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,345 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,361 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,431 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,441 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,446 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,555 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,661 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,667 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,674 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,684 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,689 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,694 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,701 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,705 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,710 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,716 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,722 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,728 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,734 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,740 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,749 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,754 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,763 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,768 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,774 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,780 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,785 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,792 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,797 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,804 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,813 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,818 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,827 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,834 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,840 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,845 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,850 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,854 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,860 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,866 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,872 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,877 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,883 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,890 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,901 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,912 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,917 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,921 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,928 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,942 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,953 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,958 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,964 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,969 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,974 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,980 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,986 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,991 [pN:job_handler_0,p:9,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 2024-09-12 12:47:14,999 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,005 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,013 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,017 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,023 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,030 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,034 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,039 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,045 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,054 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,059 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,066 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,072 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,078 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,088 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,101 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,107 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,114 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,286 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,403 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,508 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,514 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,520 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,609 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,613 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,618 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,625 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,638 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,645 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,651 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,657 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,668 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,673 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,768 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,861 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,866 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,875 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,880 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,886 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,894 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,899 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,915 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,920 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,926 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,957 [pN:job_handler_0,p:9,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 2024-09-12 12:47:15,996 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,002 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,009 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,019 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,026 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,038 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,049 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,066 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,081 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,180 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,193 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,197 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,206 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,211 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,218 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,244 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,250 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,328 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,329 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,335 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,345 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,423 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,428 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,439 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,444 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,456 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,465 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,478 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,485 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,548 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,577 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,584 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,589 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,593 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,599 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,604 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,608 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,613 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,618 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,619 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,624 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,627 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,629 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,636 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,647 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,656 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,663 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,671 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,680 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,685 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,691 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,696 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,701 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,757 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,784 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,790 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,794 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,799 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,800 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,806 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,812 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,818 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,824 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,829 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,831 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,835 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,837 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,843 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,848 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,853 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,859 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,865 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,871 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,877 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,882 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,888 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,894 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,899 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,904 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,911 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,916 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,923 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,929 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,934 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,941 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,949 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,955 [pN:job_handler_0,p:9,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 2024-09-12 12:47:16,963 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,037 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,043 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,049 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,056 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,064 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,092 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,098 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,434 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,444 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,452 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,461 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,468 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,475 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,503 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,512 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,521 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,526 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,569 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,575 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,580 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,589 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,592 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,592 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,595 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,607 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,617 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,619 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,619 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,623 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,636 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,647 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,652 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,657 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,664 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,670 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,674 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,679 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,684 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,691 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,846 [pN:job_handler_0,p:9,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 2024-09-12 12:47:17,996 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,317 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,331 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,337 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,344 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,349 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,361 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,448 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,454 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,460 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,466 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,471 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,478 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,483 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,489 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,496 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,504 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,510 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,518 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,524 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,531 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,539 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,546 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,553 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,560 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,565 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,570 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,576 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,581 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,586 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,592 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,600 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,606 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,613 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,618 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,623 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,628 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,634 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,640 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,646 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,651 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,657 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,665 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,670 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,678 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,685 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,690 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,697 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,703 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,712 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,718 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,725 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,731 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,737 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,743 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,749 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,755 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,761 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,766 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,771 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,778 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,783 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,790 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,797 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,803 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,810 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,817 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,822 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,829 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,835 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,843 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,851 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,857 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,865 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,873 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,878 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,884 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,890 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,895 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,900 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,907 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,913 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,917 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,923 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,928 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,933 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,939 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,945 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,950 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,955 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,960 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,969 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,974 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,979 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,985 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,991 [pN:job_handler_0,p:9,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 2024-09-12 12:47:18,996 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,002 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,007 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,013 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,018 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,027 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,032 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,039 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,045 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,052 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,057 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,064 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,071 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,078 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,083 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,091 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,098 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,132 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,168 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,182 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,188 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,193 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,198 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,203 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,209 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,214 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,228 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,234 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,250 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,260 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,296 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,323 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,329 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,336 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,341 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,347 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,403 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,453 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,483 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,516 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,542 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,547 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,552 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,574 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,594 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,599 [pN:job_handler_0,p:9,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. +galaxy.tool_util.toolbox.base WARNING 2024-09-12 12:47:19,637 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,717 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,724 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,731 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,739 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,745 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,752 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,758 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,766 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,772 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,781 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,789 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,798 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,805 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,815 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,825 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,830 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,842 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,852 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,866 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,874 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,970 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,978 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,984 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,989 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,996 [pN:job_handler_0,p:9,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 2024-09-12 12:47:19,999 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,005 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,011 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,018 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,023 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,025 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,032 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,038 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,045 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,052 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,059 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,065 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,073 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,080 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,087 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,096 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,096 [pN:job_handler_0,p:9,tN:MainThread] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-09-12 12:47:20,097 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,097 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,097 [pN:job_handler_0,p:9,tN:MainThread] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,097 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,097 [pN:job_handler_0,p:9,tN:MainThread] Reading tools from config files finished (9126.295 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,098 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,098 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,098 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,098 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,099 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,099 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,099 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,099 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,099 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,099 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,100 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,101 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,102 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,103 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,104 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,105 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,106 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,107 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,108 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,109 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,110 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,111 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,112 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,tN:MainThread] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,113 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,114 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,tN:MainThread] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,115 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,116 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,117 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,117 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,117 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,117 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,117 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,117 [pN:job_handler_0,p:9,tN:MainThread] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,118 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,tN:MainThread] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,119 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,120 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,121 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,122 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,123 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,124 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,125 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,tN:MainThread] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,126 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,127 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,128 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,129 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,130 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,130 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,130 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,130 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,130 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,131 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,132 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,132 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,132 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,132 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,133 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,134 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,135 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,136 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,tN:MainThread] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,137 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,138 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,139 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,140 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,141 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,142 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,143 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,143 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,143 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,143 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,143 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,144 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,145 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,145 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,145 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,145 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,145 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,145 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,146 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,147 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,148 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,149 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,150 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,151 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,152 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,153 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,154 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,155 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,156 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,157 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,158 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,159 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,160 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,161 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,162 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,tN:MainThread] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,tN:MainThread] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,163 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,164 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,165 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,166 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,167 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,168 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,169 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,170 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,171 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,172 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,173 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,174 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,175 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,176 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,177 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,177 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,177 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,177 [pN:job_handler_0,p:9,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.... 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[pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] Loading section: EMBOSS +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,185 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,tN:MainThread] Loading section: GEMINI +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,tN:MainThread] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,186 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,187 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,188 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,188 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,188 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__extract_reads/qiime2__feature_classifier__extract_reads/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 2024-09-12 12:47:20,192 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/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 2024-09-12 12:47:20,192 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/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 2024-09-12 12:47:20,192 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,192 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,192 [pN:job_handler_0,p:9,tN:MainThread] 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.... 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,209 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,209 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,209 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,209 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,209 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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12:47:20,211 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,211 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,211 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,211 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,211 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,212 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,213 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,214 [pN:job_handler_0,p:9,tN:MainThread] Loading tool panel finished (116.546 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,221 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,222 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,222 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,222 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,222 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,222 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,222 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,223 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,224 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,224 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,224 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,224 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,224 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,225 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,226 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,226 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,226 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,226 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,226 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,227 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,228 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,229 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,230 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,231 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,232 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,232 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,232 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,232 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,232 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,233 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,234 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,234 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,234 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,235 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,236 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,236 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,236 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,236 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,237 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,237 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,237 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,237 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,237 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,237 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,238 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,239 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,240 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,241 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,241 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,241 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,241 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,241 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,241 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,242 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,243 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,244 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,245 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,246 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,247 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,248 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,249 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,249 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,249 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,249 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,249 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,249 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,250 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,251 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,252 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,252 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,252 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,252 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,252 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,252 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,253 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,253 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,253 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,253 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,253 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,253 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,254 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,254 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,254 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,254 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,254 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,255 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,256 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,257 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,258 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,259 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,259 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,259 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,259 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,259 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,259 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,260 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,260 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,260 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,260 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,260 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,261 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,262 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,263 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,264 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,265 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,266 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,266 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,266 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,266 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,266 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,266 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,267 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,268 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,268 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,268 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,268 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,268 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,268 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,269 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,269 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,269 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,269 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,269 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,270 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,271 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,272 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,273 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,274 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,275 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,275 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,275 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,275 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,275 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,275 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,276 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,277 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,278 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,279 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,280 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,281 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,282 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,283 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,284 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,285 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,286 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,286 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,286 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,286 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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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 2024-09-12 12:47:20,287 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,287 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,287 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,287 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,287 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,288 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,289 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,290 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,291 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,292 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,292 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,292 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,292 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,292 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,292 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,293 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,293 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,293 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,293 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,293 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,294 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,295 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,296 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,297 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,298 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,298 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,298 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,298 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,298 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,298 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,299 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,300 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,301 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,301 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,301 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,301 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,301 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,301 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,302 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,303 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,304 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,304 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,304 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,304 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,305 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,306 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,307 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,308 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,309 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,310 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,311 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,312 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,313 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,314 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,315 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,316 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,316 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,316 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,316 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,316 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,316 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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[pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,324 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,325 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,325 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,325 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,325 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,325 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,325 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,326 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,327 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,329 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,329 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,329 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,330 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,330 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,330 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,330 [pN:job_handler_0,p:9,tN:MainThread] Loaded 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[pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.10.3+galaxy1, version: 0.10.3+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,340 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3, version: 0.2.3+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,341 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy3, version: 0.2.3+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,341 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy3, version: 0.2.3+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,341 [pN:job_handler_0,p:9,tN:MainThread] Loaded 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-12 12:47:20,346 [pN:job_handler_0,p:9,tN:MainThread] Loading EDAM tool panel finished (131.605 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,352 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,353 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,354 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,354 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,354 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,354 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,354 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,354 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,355 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,356 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,357 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,358 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,359 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,360 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,361 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,361 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,361 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,362 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,363 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,364 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,365 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,366 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,367 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,368 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,369 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,370 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,371 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,372 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,373 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,374 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,375 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,376 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,377 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,378 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,379 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,380 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,381 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,382 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,383 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,384 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,385 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,386 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,387 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,388 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,389 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,390 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,391 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,392 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,393 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,394 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,395 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,396 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,397 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,398 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,399 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,400 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,401 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,402 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,403 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,404 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,405 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,406 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,407 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,408 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,409 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,410 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,411 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,412 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,413 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,414 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,415 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,415 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,415 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,415 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,415 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,415 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,416 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,417 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,418 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,419 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,420 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,421 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,422 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,423 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,423 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,423 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,423 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,423 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,423 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,424 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,424 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,424 [pN:job_handler_0,p:9,tN:MainThread] 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 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,427 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,427 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,427 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,427 [pN:job_handler_0,p:9,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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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,429 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,429 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,429 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,430 [pN:job_handler_0,p:9,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 2024-09-12 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version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,432 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,433 [pN:job_handler_0,p:9,tN:MainThread] Loaded 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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 2024-09-12 12:47:20,449 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,449 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,449 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,449 [pN:job_handler_0,p:9,tN:MainThread] 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 2024-09-12 12:47:20,449 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,449 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,450 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,451 [pN:job_handler_0,p:9,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:47:20,451 [pN:job_handler_0,p:9,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-12 12:47:20,451 [pN:job_handler_0,p:9,tN:MainThread] Loading EDAM tool panel finished (104.254 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2024-09-12 12:47:20,451 [pN:job_handler_0,p:9,tN:MainThread] Writing integrated tool panel config file to '/galaxy/server/config/mutable/integrated_tool_panel.xml' +galaxy.tool_util.deps.installable WARNING 2024-09-12 12:47:20,470 [pN:job_handler_0,p:9,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.installable WARNING 2024-09-12 12:47:20,476 [pN:job_handler_0,p:9,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.containers DEBUG 2024-09-12 12:47:20,477 [pN:job_handler_0,p:9,tN:MainThread] Loading container resolution config from file '/galaxy/server/config/container_resolvers_conf.xml' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,494 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,494 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,495 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,496 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,496 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,496 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,497 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,498 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,498 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,500 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,500 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,501 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,501 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,502 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,503 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,504 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,504 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,506 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,507 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,508 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,508 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,509 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,509 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,509 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,511 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,512 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,513 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,513 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,514 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,514 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,515 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,516 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,516 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,517 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,517 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,517 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,517 [pN:job_handler_0,p:9,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,518 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,519 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,520 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,520 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,520 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,520 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,520 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,521 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,522 [pN:job_handler_0,p:9,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,525 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,526 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,527 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,527 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,528 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,529 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,530 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,531 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,532 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,533 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,534 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,535 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,536 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,536 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,538 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,539 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,540 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,540 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,541 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,543 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,544 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,546 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,547 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,548 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,549 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,550 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,551 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,552 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,552 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,553 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,554 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,555 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,556 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,557 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,558 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,559 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,560 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,560 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,561 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,562 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,563 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,564 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,565 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,566 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,567 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,568 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,569 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,569 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,571 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,571 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,572 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,573 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,574 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,575 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,576 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,577 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,578 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,579 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,579 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,581 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,582 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,583 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,584 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,585 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,585 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,586 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,587 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,588 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,589 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,589 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,591 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,592 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,593 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,594 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,594 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,596 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,596 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,597 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,598 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,599 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,600 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,601 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,602 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,603 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,604 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,605 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,607 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,608 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,608 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,609 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,610 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,611 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,612 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,613 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,614 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,615 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,617 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,618 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,619 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,619 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,620 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,621 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,622 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,623 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,625 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,626 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,627 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,627 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,628 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,629 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,630 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,631 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,632 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,633 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,634 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,636 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,637 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,639 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,640 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,641 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,643 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,644 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,645 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,647 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,648 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,650 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,651 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,652 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,654 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,655 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,657 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,658 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,660 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,661 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,663 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,664 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,666 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,667 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,668 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,669 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,670 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,672 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,673 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,675 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,676 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,677 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,677 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,678 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,680 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,681 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,682 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,683 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,683 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,684 [pN:job_handler_0,p:9,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-09-12 12:47:20,686 [pN:job_handler_0,p:9,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:47:20,687 [pN:job_handler_0,p:9,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:47:20,688 [pN:job_handler_0,p:9,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:47:20,689 [pN:job_handler_0,p:9,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:47:20,690 [pN:job_handler_0,p:9,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +sqlitedict DEBUG 2024-09-12 12:47:20,692 [pN:job_handler_0,p:9,tN:MainThread] closing SqliteDict(/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite) +sqlitedict.SqliteMultithread DEBUG 2024-09-12 12:47:20,693 [pN:job_handler_0,p:9,tN:Thread-2] received: --close--, send: --no more-- +sqlitedict DEBUG 2024-09-12 12:47:20,693 [pN:job_handler_0,p:9,tN:MainThread] opening Sqlite table 'unnamed' in '/cvmfs/cloud.galaxyproject.org/var/tool_cache/cache.sqlite' +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,699 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,700 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,700 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,701 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,701 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,701 [pN:job_handler_0,p:9,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,702 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,702 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,703 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,704 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,704 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,705 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,706 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,706 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,707 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,707 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,707 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,710 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,712 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,712 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,713 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,713 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,714 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,716 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,718 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,720 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,724 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,726 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,726 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,727 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,727 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,727 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,728 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,728 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,729 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,730 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,731 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,733 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,736 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,739 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,742 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,744 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,747 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,749 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,751 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,753 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,755 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,757 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,760 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,762 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,763 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,763 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,764 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,765 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,765 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,766 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,767 [pN:job_handler_0,p:9,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,767 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,768 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.config_parser INFO 2024-09-12 12:47:20,768 [pN:job_handler_0,p:9,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,768 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2024-09-12 12:47:20,769 [pN:job_handler_0,p:9,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2024-09-12 12:47:20,783 [pN:job_handler_0,p:9,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2024-09-12 12:47:20,793 [pN:job_handler_0,p:9,tN:MainThread] Loaded tour 'core.windows' +galaxy.tours._impl INFO 2024-09-12 12:47:20,809 [pN:job_handler_0,p:9,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2024-09-12 12:47:20,830 [pN:job_handler_0,p:9,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2024-09-12 12:47:20,835 [pN:job_handler_0,p:9,tN:MainThread] Initializing job handler +galaxy.jobs INFO 2024-09-12 12:47:20,835 [pN:job_handler_0,p:9,tN:MainThread] Handler 'job_handler_0' will load all configured runner plugins +galaxy.jobs.runners DEBUG 2024-09-12 12:47:20,837 [pN:job_handler_0,p:9,tN:MainThread] Loading KubernetesRunner with params: {'k8s_cleanup_job': 'onsuccess', 'k8s_fs_group_id': '101', 'k8s_galaxy_instance_id': 'prod-24-09-12-12-33-1-galaxy', 'k8s_interactivetools_ingress_annotations': '\nnginx.ingress.kubernetes.io/auth-tls-pass-certificate-to-upstream: "true"\nnginx.ingress.kubernetes.io/auth-tls-secret: \'prod-24-09-12-12-33-1/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': 'prod-24-09-12-12-33-1', 'k8s_node_selector': 'cloud.google.com/gke-nodepool: default-pool', 'k8s_persistent_volume_claims': 'prod-24-09-12-12-33-1-galaxy-galaxy-pvc:/galaxy/server/database,prod-24-09-12-12-33-1-galaxy-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org,prod-24-09-12-12-33-1-galaxy-galaxy-pvc/cvmfsclone:/cvmfs/cloud.galaxyproject.org', 'k8s_pod_priority_class': 'prod-24-09-12-12-33-1-priority-class', 'k8s_pull_policy': 'IfNotPresent', 'k8s_supplemental_group_id': '101', 'k8s_use_service_account': True} +galaxy.jobs.runners.state_handler_factory DEBUG 2024-09-12 12:47:20,838 [pN:job_handler_0,p:9,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners.util.pykube_util ERROR 2024-09-12 12:47:20,839 [pN:job_handler_0,p:9,tN:MainThread] Galaxy instance [prod-24-09-12-12-33-1-galaxy] is either too long (>20 characters) or it includes non DNS acceptable characters, ignoring it. +galaxy.jobs DEBUG 2024-09-12 12:47:20,839 [pN:job_handler_0,p:9,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.kubernetes:KubernetesJobRunner' as 'k8s' +galaxy.jobs.runners.state_handler_factory DEBUG 2024-09-12 12:47:20,840 [pN:job_handler_0,p:9,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2024-09-12 12:47:20,840 [pN:job_handler_0,p:9,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.handler DEBUG 2024-09-12 12:47:20,840 [pN:job_handler_0,p:9,tN:MainThread] Loaded job runners plugins: k8s:local +galaxy.jobs.runners DEBUG 2024-09-12 12:47:20,845 [pN:job_handler_0,p:9,tN:MainThread] Starting 4 KubernetesRunner workers +galaxy.jobs.runners DEBUG 2024-09-12 12:47:20,846 [pN:job_handler_0,p:9,tN:MainThread] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2024-09-12 12:47:20,848 [pN:job_handler_0,p:9,tN:MainThread] Handler queue starting for jobs assigned to handler: job_handler_0 +galaxy.jobs.handler INFO 2024-09-12 12:47:20,863 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,865 [pN:job_handler_0,p:9,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2024-09-12 12:47:20,865 [pN:job_handler_0,p:9,tN:MainThread] job handler stop queue started +galaxy.web_stack.handlers DEBUG 2024-09-12 12:47:20,884 [pN:job_handler_0,p:9,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-09-12 12:47:20,884 [pN:job_handler_0,p:9,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-09-12 12:47:20,884 [pN:job_handler_0,p:9,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.web_stack.handlers INFO 2024-09-12 12:47:20,899 [pN:job_handler_0,p:9,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 2024-09-12 12:47:20,899 [pN:job_handler_0,p:9,tN:MainThread] Workflow scheduling handler assignment method(s): db-skip-locked +galaxy.workflow.scheduling_manager INFO 2024-09-12 12:47:20,899 [pN:job_handler_0,p:9,tN:MainThread] Tag [schedulers] handlers: workflow_scheduler0 +galaxy.web_stack.handlers DEBUG 2024-09-12 12:47:20,899 [pN:job_handler_0,p:9,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.queue_worker INFO 2024-09-12 12:47:20,915 [pN:job_handler_0,p:9,tN:MainThread] Binding and starting galaxy control worker for job_handler_0 +galaxy.queue_worker INFO 2024-09-12 12:47:20,921 [pN:job_handler_0,p:9,tN:MainThread] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.model.database_heartbeat DEBUG 2024-09-12 12:47:20,938 [pN:job_handler_0,p:9,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is config watcher +galaxy.app INFO 2024-09-12 12:47:20,961 [pN:job_handler_0,p:9,tN:MainThread] Galaxy app startup finished (16912.621 ms) +galaxy.web_stack INFO 2024-09-12 12:47:20,961 [pN:job_handler_0,p:9,tN:MainThread] Galaxy server instance 'job_handler_0' is running +galaxy.queue_worker INFO 2024-09-12 12:47:20,970 [pN:job_handler_0,p:9,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-09-12 12:47:20,970 [pN:job_handler_0,p:9,tN:Thread-1] App is not a webapp, not building a search index +galaxy.model.database_heartbeat DEBUG 2024-09-12 12:48:20,951 [pN:job_handler_0,p:9,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is not config watcher +galaxy.queue_worker INFO 2024-09-12 12:48:22,724 [pN:job_handler_0,p:9,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-09-12 12:48:22,724 [pN:job_handler_0,p:9,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-09-12 12:48:22,750 [pN:job_handler_0,p:9,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-09-12 12:48:22,757 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,757 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,758 [pN:job_handler_0,p:9,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-09-12 12:48:22,759 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,759 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,761 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,761 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,763 [pN:job_handler_0,p:9,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 865, 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 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, 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 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, 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 2024-09-12 12:48:22,764 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,764 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,786 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,tN:Thread-1] Reading tools from config files finished (77.587 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,834 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,836 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,838 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,843 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,848 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,849 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,852 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,882 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,886 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,895 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,897 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,897 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,897 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,897 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,897 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,897 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,899 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,900 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,900 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,900 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,900 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,901 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,901 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,901 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,901 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,901 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,902 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,903 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,904 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,905 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,906 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,906 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,906 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,906 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,906 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,907 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,907 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,907 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,907 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,907 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,907 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,908 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,908 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,908 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,912 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,913 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,tN:Thread-1] Loaded 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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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,914 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,915 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,916 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into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,923 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,923 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,923 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: EMBOSS +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,923 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: GATK +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,923 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: NCBI BLAST+ +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,923 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: 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into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,924 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: QIIME2 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,924 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,924 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,924 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,924 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,924 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,925 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,925 [pN:job_handler_0,p:9,tN:Thread-1] Loaded 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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 2024-09-12 12:48:22,925 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,925 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,925 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,926 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:22,927 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__pcoa/qiime2__diversity__pcoa/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 2024-09-12 12:48:22,927 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__bioenv/qiime2__diversity__bioenv/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 2024-09-12 12:48:22,927 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__pcoa_biplot/qiime2__diversity__pcoa_biplot/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 2024-09-12 12:48:22,927 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__tsne/qiime2__diversity__tsne/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 2024-09-12 12:48:22,927 [pN:job_handler_0,p:9,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 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DEBUG 2024-09-12 12:48:22,953 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,953 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,953 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,953 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,953 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,953 [pN:job_handler_0,p:9,tN:Thread-1] Loading tool panel finished (119.097 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,961 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,961 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,961 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,961 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,961 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,967 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,968 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,974 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,977 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,978 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,979 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,984 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,986 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,986 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,986 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,986 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,986 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,994 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:22,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,004 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,005 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,006 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,007 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,008 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,009 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,010 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,011 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,012 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,013 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,014 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,014 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,014 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,014 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,014 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,015 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,015 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,015 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,015 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,015 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,015 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,016 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,016 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,016 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,016 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,016 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,016 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,017 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,018 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,018 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,018 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,018 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,018 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,019 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,020 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,020 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,020 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,020 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,020 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,021 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,022 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,023 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,024 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,025 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,026 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,027 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,028 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,029 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,030 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,031 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,032 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,033 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,034 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,035 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,036 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,036 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,036 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,036 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,036 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,036 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,037 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,038 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,039 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,040 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,041 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,041 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,041 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,041 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,041 [pN:job_handler_0,p:9,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 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[pN:job_handler_0,p:9,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 2024-09-12 12:48:23,049 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,049 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,049 [pN:job_handler_0,p:9,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 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2024-09-12 12:48:23,050 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,050 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,050 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,050 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,050 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,050 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,051 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,052 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,053 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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[pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-12 12:48:23,076 [pN:job_handler_0,p:9,tN:Thread-1] Loading EDAM tool panel finished (122.289 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,085 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,086 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,086 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,086 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,086 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,087 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,087 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,087 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,087 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,087 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,088 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,089 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,089 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,090 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,091 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,092 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,093 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,094 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,095 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,096 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,097 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,098 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,099 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,100 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,101 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,101 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,101 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,101 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,102 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,102 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,102 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,103 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,104 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,105 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,105 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,105 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,105 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,105 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,105 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,106 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,106 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,106 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,106 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,106 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,107 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,107 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,107 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,107 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,107 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,107 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,108 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,109 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,110 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,111 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,112 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,112 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,112 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,112 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,112 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,112 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,113 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,114 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,115 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,115 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,116 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,116 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,116 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,116 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,116 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,116 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,117 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,117 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,117 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,117 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,118 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,119 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,120 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,121 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,122 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,123 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,124 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,125 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,125 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,125 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,125 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,125 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,126 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,127 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,128 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,129 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,130 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,131 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,132 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,133 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,134 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,135 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,136 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,137 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,138 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,139 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,140 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,141 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,142 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,143 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,144 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,145 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,146 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,146 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,146 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,146 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,146 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,146 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,147 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,148 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,149 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,150 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,151 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,152 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,152 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,152 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,152 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,152 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,152 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,153 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,153 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,153 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,153 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,153 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,154 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,154 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,154 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,154 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,154 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,154 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,155 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,155 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,155 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,155 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,155 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,155 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,156 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,157 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,158 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,159 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,160 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,161 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,162 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,163 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,164 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,164 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,164 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,164 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,164 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,164 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,165 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,166 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,167 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,168 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,169 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,170 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,171 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,172 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,173 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,173 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,173 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,173 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,173 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,173 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,174 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,174 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,174 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,174 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,174 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,175 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,175 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,175 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,175 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,175 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,175 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,176 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,177 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,178 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,179 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,179 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[pN:job_handler_0,p:9,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 2024-09-12 12:48:23,192 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,193 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,193 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,213 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,213 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,213 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,213 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,214 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,215 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,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 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Loading EDAM tool panel finished (139.831 ms) +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,216 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,217 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,218 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,219 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,220 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,221 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,222 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,223 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,224 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,225 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,226 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:23,228 [pN:job_handler_0,p:9,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:23,229 [pN:job_handler_0,p:9,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:23,230 [pN:job_handler_0,p:9,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:23,232 [pN:job_handler_0,p:9,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:23,233 [pN:job_handler_0,p:9,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-09-12 12:48:23,233 [pN:job_handler_0,p:9,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-09-12 12:48:23,234 [pN:job_handler_0,p:9,tN:Thread-1] Toolbox reload (510.290 ms) +galaxy.queue_worker INFO 2024-09-12 12:48:23,235 [pN:job_handler_0,p:9,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-09-12 12:48:23,235 [pN:job_handler_0,p:9,tN:Thread-1] App is not a webapp, not building a search index +galaxy.queue_worker INFO 2024-09-12 12:48:52,523 [pN:job_handler_0,p:9,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-09-12 12:48:52,523 [pN:job_handler_0,p:9,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-09-12 12:48:52,553 [pN:job_handler_0,p:9,tN:Thread-1] directory not found: /galaxy/server/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2024-09-12 12:48:52,562 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,562 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,562 [pN:job_handler_0,p:9,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-09-12 12:48:52,563 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,563 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,566 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,566 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,567 [pN:job_handler_0,p:9,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 865, 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 1092, in load_tool + tool = self.create_tool( + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 530, 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 546, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 802, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 799, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1123, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem + param = ToolParameter.build(self, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 319, in build + return parameter_types[param_type](tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2044, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1832, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 178, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 50, in from_element + return validator_types[_type].from_element(param, elem) + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 727, 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 2024-09-12 12:48:52,568 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,568 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,590 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,637 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,tN:Thread-1] Reading tools from config files finished (76.855 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,638 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,639 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,640 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,641 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,642 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,643 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,644 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,645 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,646 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,647 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,648 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,649 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,650 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,650 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,650 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,650 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,650 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,651 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,652 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,652 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,652 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,652 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,652 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,652 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,653 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,654 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,655 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,656 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,657 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,658 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,658 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,658 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,658 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,659 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,659 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,659 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,659 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,659 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,659 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,660 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,660 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,660 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,660 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,660 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,661 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,662 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,663 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,664 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,665 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,666 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,666 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,666 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,666 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,666 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,667 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,667 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,667 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,667 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,667 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,667 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,668 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,669 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,670 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,671 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,672 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,673 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,674 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,675 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,676 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,676 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,676 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,676 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,676 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,676 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,677 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,677 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,677 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,677 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,677 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,677 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,678 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,679 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,680 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,680 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,680 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,680 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,680 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,680 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,681 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,681 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,681 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,681 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,681 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,681 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,682 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,683 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,684 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,685 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,686 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,687 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,688 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,689 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,690 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,691 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,691 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,691 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,691 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,691 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,691 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,692 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,693 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,694 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,694 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,694 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,694 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,694 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,694 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,695 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,696 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,697 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,698 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,699 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,700 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,700 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,700 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,700 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,700 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,701 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,702 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,703 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,704 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,705 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,706 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,706 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,706 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,706 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,706 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,707 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,708 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,708 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,708 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,708 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,708 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,708 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,709 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,710 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,711 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,712 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,712 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,712 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,712 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,713 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,713 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,713 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,713 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,713 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,713 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,714 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,715 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,715 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,715 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,715 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,715 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,715 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,716 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,716 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,716 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,716 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,716 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,716 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,717 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,717 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,717 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,717 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,717 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,718 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,719 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,720 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,721 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,722 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,723 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,723 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,723 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,723 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,723 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,723 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,724 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,725 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,726 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,726 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,726 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,727 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,728 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,729 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,730 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,731 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,731 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,731 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,731 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,731 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,731 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,732 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,732 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,732 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,732 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,732 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,732 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,733 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,734 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,735 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,735 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,735 [pN:job_handler_0,p:9,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: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,736 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,736 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,736 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,736 [pN:job_handler_0,p:9,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.... 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version: 3.5.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,749 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,749 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,749 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,749 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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[pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/qiime2__feature_classifier__classify_consensus_vsearch/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 2024-09-12 12:48:52,756 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,756 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,756 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version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,780 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,781 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,781 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,781 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,781 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,781 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,782 [pN:job_handler_0,p:9,tN:Thread-1] Loading tool panel finished (143.984 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,791 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,791 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,791 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,791 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,792 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,792 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,793 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,794 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,794 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,794 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,794 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,795 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,795 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,795 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,796 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,796 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,796 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,797 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,797 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,797 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,797 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,797 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,798 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,798 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,798 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,798 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,799 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,799 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,799 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,799 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,799 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,800 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,800 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,800 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,800 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,800 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,800 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,801 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,802 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,802 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,802 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,802 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,802 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,802 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,803 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,803 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,803 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,803 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,803 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,803 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,804 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,805 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,806 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,806 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,806 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,806 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,807 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,807 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,807 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,807 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,807 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,807 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,808 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,808 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,808 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,808 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,809 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,810 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,810 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,810 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,810 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,810 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,811 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,811 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,811 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,811 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,812 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,813 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,814 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,815 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,816 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,817 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,818 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,819 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,820 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,821 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,821 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,821 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,821 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,821 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,822 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,822 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,822 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,822 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,822 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,823 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,824 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,824 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,824 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,824 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,824 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,824 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,825 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,826 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,827 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,827 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,827 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,827 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,827 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,827 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,828 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,829 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,829 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,829 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,829 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,829 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,830 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,830 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,830 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,830 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,830 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,830 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,831 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,831 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,831 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,831 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,831 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,832 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,833 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,834 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,835 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,836 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,837 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,838 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,839 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,840 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,841 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,842 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,843 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,844 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,845 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,846 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,847 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,848 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,849 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,850 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,851 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,852 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,853 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,854 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,855 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,856 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,857 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,858 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,859 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,860 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,861 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,862 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,863 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,864 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,865 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,866 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,867 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,868 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,869 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,870 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,871 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,872 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,873 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,874 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,875 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,876 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,877 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,878 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,879 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,880 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,881 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,882 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,883 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,884 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,885 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,886 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,887 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,888 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,889 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,890 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,891 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,892 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,893 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,894 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,895 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,895 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,896 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,896 [pN:job_handler_0,p:9,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 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[pN:job_handler_0,p:9,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 2024-09-12 12:48:52,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,898 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,898 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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2024-09-12 12:48:52,909 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,910 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,911 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,911 [pN:job_handler_0,p:9,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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+galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,948 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,948 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,948 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,948 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,948 [pN:job_handler_0,p:9,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,949 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-12 12:48:52,949 [pN:job_handler_0,p:9,tN:Thread-1] Loading EDAM tool panel finished (166.271 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,957 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,957 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,957 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,957 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,958 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,958 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,958 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,958 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,958 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,959 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,959 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,959 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,959 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,959 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,959 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,960 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,960 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,960 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,960 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,961 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,962 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,963 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,964 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,965 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,966 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,967 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,968 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,968 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,968 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,968 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,968 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,968 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,969 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,969 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,969 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,969 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,969 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,970 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,971 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,972 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,973 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,974 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,975 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,976 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,977 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,978 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,979 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,980 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,981 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,982 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,983 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,984 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,985 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,986 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,987 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,988 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,989 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,990 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,991 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,992 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,993 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,994 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:52,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,995 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,996 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,997 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,998 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:52,999 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,000 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,001 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,002 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,003 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,338 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,338 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,339 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,339 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,339 [pN:job_handler_0,p:9,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. +sqlitedict.SqliteMultithread DEBUG 2024-09-12 12:48:53,340 [pN:job_handler_0,p:9,tN:Thread-3] received: --close--, send: --no more-- +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,345 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,346 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,347 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,347 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,347 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,348 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,348 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,348 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,348 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,348 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,348 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,349 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,349 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,349 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,349 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,349 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,349 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,350 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,351 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,352 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,353 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,353 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,354 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,356 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,356 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,356 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,356 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,356 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,356 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,357 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,357 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,357 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,357 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,358 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,358 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,358 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,360 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,360 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,360 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,360 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,360 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,360 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,361 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,362 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,362 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,363 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,363 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,364 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,364 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,364 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,364 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,364 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,365 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,365 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,365 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,365 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,365 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,366 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,367 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,367 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,367 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,368 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,368 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,368 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,368 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,369 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,370 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,370 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,370 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,370 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,370 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,370 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,371 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,372 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,373 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,374 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,375 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,376 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,376 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,376 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,376 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,376 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,376 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,377 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,377 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,377 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,377 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,377 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,377 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,378 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,378 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,378 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,378 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,378 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,379 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,380 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,381 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,382 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,383 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,384 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,385 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,386 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,387 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,388 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,389 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,390 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,391 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,392 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,392 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,392 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,392 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,392 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,393 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,393 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,393 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,393 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,394 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,395 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,396 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,397 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,398 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,399 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,400 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,400 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,400 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,400 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,400 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,400 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,401 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,401 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,401 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,401 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,401 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,401 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,402 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,403 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,404 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,405 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,405 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,405 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,405 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,405 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,405 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,406 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,407 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,tN:Thread-1] 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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,408 [pN:job_handler_0,p:9,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.... 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[pN:job_handler_0,p:9,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 2024-09-12 12:48:53,419 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,419 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,419 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: 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DEBUG 2024-09-12 12:48:53,422 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,422 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,422 [pN:job_handler_0,p:9,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 2024-09-12 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toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.9.3+galaxy0, version: 1.9.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,436 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.9.3+galaxy0, version: 1.9.3+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_NVC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3, version: 2.6.4.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,437 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,438 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,438 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,438 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,438 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,438 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,438 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,439 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,440 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,440 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,440 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,440 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,440 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,440 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,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 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,tN:Thread-1] Loading EDAM tool panel finished (491.994 ms) +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,441 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,442 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,443 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,444 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,445 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,446 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,447 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,448 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,449 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,450 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,451 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,452 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,453 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,454 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,454 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,454 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,454 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,454 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,454 [pN:job_handler_0,p:9,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-09-12 12:48:53,455 [pN:job_handler_0,p:9,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:53,456 [pN:job_handler_0,p:9,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:53,457 [pN:job_handler_0,p:9,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:53,458 [pN:job_handler_0,p:9,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-12 12:48:53,460 [pN:job_handler_0,p:9,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-09-12 12:48:53,460 [pN:job_handler_0,p:9,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-09-12 12:48:53,461 [pN:job_handler_0,p:9,tN:Thread-1] Toolbox reload (937.914 ms) +galaxy.queue_worker INFO 2024-09-12 12:48:53,462 [pN:job_handler_0,p:9,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-09-12 12:48:53,462 [pN:job_handler_0,p:9,tN:Thread-1] App is not a webapp, not building a search index +galaxy.jobs.handler DEBUG 2024-09-12 12:49:42,573 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 1 +tpv.rules.gateway INFO 2024-09-12 12:49:42,617 [pN:job_handler_0,p:9,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 2024-09-12 12:49:43,125 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Watching for changes in file: lib/galaxy/jobs/rules/tpv_rules_local.yml +tpv.core.entities DEBUG 2024-09-12 12:49:43,264 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:49:43,265 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:49:43,283 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:49:43,310 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:49:43,358 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (1) Working directory for job is: /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs.runners DEBUG 2024-09-12 12:49:43,369 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [1] queued (86.112 ms) +galaxy.jobs.handler INFO 2024-09-12 12:49:43,376 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:49:43,382 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 1 +galaxy.jobs DEBUG 2024-09-12 12:49:43,559 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [1] prepared (155.739 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:49:43,589 [pN:job_handler_0,p:9,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/f/4/7/dataset_f4769b91-8e52-4976-9b04-2800fe84b398_files:/galaxy/server/database/objects/f/4/7/dataset_f4769b91-8e52-4976-9b04-2800fe84b398.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:49:43,612 [pN:job_handler_0,p:9,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 ERROR 2024-09-12 12:50:21,918 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-vl57b + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-vl57b": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:50:21,980 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (1/gxy-vl57b) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-12 12:50:23,319 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 2 +tpv.core.entities DEBUG 2024-09-12 12:50:23,356 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:50:23,356 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:50:23,361 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:50:23,377 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:50:23,396 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs.runners DEBUG 2024-09-12 12:50:23,404 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [2] queued (43.093 ms) +galaxy.jobs.handler INFO 2024-09-12 12:50:23,408 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:50:23,413 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 2 +galaxy.jobs DEBUG 2024-09-12 12:50:23,524 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [2] prepared (91.488 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:50:23,545 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/2/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/2/registry.xml' '/galaxy/server/database/jobs_directory/000/2/upload_params.json' '2:/galaxy/server/database/objects/9/c/2/dataset_9c24e152-6edd-41bd-9bce-ab69133f9801_files:/galaxy/server/database/objects/9/c/2/dataset_9c24e152-6edd-41bd-9bce-ab69133f9801.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:50:23,560 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:50:32,253 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 2: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:50:38,481 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 2 finished +galaxy.model.metadata DEBUG 2024-09-12 12:50:38,540 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.jobs INFO 2024-09-12 12:50:38,593 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 2 in /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs DEBUG 2024-09-12 12:50:38,645 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 2 executed (137.477 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:50:39,845 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 3 +tpv.core.entities DEBUG 2024-09-12 12:50:39,893 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:50:39,893 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:50:39,899 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:50:39,913 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (3) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:50:39,934 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (3) Working directory for job is: /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs.runners DEBUG 2024-09-12 12:50:39,944 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [3] queued (44.844 ms) +galaxy.jobs.handler INFO 2024-09-12 12:50:39,948 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:50:39,952 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 3 +galaxy.jobs DEBUG 2024-09-12 12:50:40,033 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [3] prepared (62.879 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:50:40,034 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:50:40,034 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0: python:3.10.4 +galaxy.tool_util.deps.mulled.util DEBUG 2024-09-12 12:50:40,036 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Querying https://quay.io/api/v1/repository for repos within biocontainers +galaxy.tool_util.deps.containers INFO 2024-09-12 12:51:04,676 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.10.4,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:51:04,700 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/3/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/2040e4c2750a/column_remove_by_header/column_remove_by_header.py' -i '/galaxy/server/database/objects/9/c/2/dataset_9c24e152-6edd-41bd-9bce-ab69133f9801.dat' -o '/galaxy/server/database/objects/4/5/7/dataset_45747e63-703c-4d81-af9d-856d8f1ea040.dat' -d ' ' --keep -s '#' --unicode-escaped-cols --columns 'KEY' 'a'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:04,726 [pN:job_handler_0,p:9,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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:51:04,752 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:51:04,752 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0: python:3.10.4 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:51:04,773 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.10.4,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:14,525 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 3: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:51:20,594 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 3 finished +galaxy.model.metadata DEBUG 2024-09-12 12:51:20,653 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.jobs INFO 2024-09-12 12:51:20,693 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 3 in /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs DEBUG 2024-09-12 12:51:20,736 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 3 executed (113.356 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:51:23,124 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 5, 4 +tpv.core.entities DEBUG 2024-09-12 12:51:23,164 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:23,165 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (4) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:23,170 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (4) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:23,184 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (4) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:23,201 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (4) Working directory for job is: /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:23,209 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [4] queued (38.833 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:23,212 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:23,217 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 4 +tpv.core.entities DEBUG 2024-09-12 12:51:23,230 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:23,231 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:23,237 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:23,253 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:23,284 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (5) Working directory for job is: /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:23,292 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [5] queued (55.086 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:23,296 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:23,301 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 5 +galaxy.jobs DEBUG 2024-09-12 12:51:23,345 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [4] prepared (103.760 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:23,376 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/4/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/4/registry.xml' '/galaxy/server/database/jobs_directory/000/4/upload_params.json' '4:/galaxy/server/database/objects/c/f/4/dataset_cf416458-5935-48a0-a2fa-daa31df45f41_files:/galaxy/server/database/objects/c/f/4/dataset_cf416458-5935-48a0-a2fa-daa31df45f41.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:23,390 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:51:23,435 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [5] prepared (110.767 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:23,459 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/5/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/5/registry.xml' '/galaxy/server/database/jobs_directory/000/5/upload_params.json' '5:/galaxy/server/database/objects/0/0/f/dataset_00fe3e1e-b737-4f43-baf1-f6e3e3cff424_files:/galaxy/server/database/objects/0/0/f/dataset_00fe3e1e-b737-4f43-baf1-f6e3e3cff424.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:23,472 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (5) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:51:24,298 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8, 7, 6 +tpv.core.entities DEBUG 2024-09-12 12:51:24,342 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:24,343 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:24,350 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:24,371 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:24,400 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (6) Working directory for job is: /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:24,408 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [6] queued (58.142 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:24,416 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:24,420 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 6 +tpv.core.entities DEBUG 2024-09-12 12:51:24,442 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:24,443 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:24,452 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:24,481 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:24,530 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (7) Working directory for job is: /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:24,540 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [7] queued (88.672 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:24,547 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:24,566 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 7 +tpv.core.entities DEBUG 2024-09-12 12:51:24,573 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:24,574 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:24,586 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:24,608 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [6] prepared (148.343 ms) +galaxy.jobs DEBUG 2024-09-12 12:51:24,615 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:24,638 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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/a/4/d/dataset_a4d544df-261d-451c-b42a-a83cf1391bea_files:/galaxy/server/database/objects/a/4/d/dataset_a4d544df-261d-451c-b42a-a83cf1391bea.dat'] +galaxy.jobs DEBUG 2024-09-12 12:51:24,655 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (8) Working directory for job is: /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:24,660 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:51:24,666 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [8] queued (79.288 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:24,669 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:24,679 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 8 +galaxy.jobs DEBUG 2024-09-12 12:51:24,735 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [7] prepared (138.570 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:24,768 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/7/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/7/registry.xml' '/galaxy/server/database/jobs_directory/000/7/upload_params.json' '7:/galaxy/server/database/objects/8/b/e/dataset_8be2a7ac-7427-428e-ac7a-c1e026b7b59b_files:/galaxy/server/database/objects/8/b/e/dataset_8be2a7ac-7427-428e-ac7a-c1e026b7b59b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:24,800 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (7) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:51:24,840 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [8] prepared (124.498 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:24,862 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/8/registry.xml' '/galaxy/server/database/jobs_directory/000/8/upload_params.json' '8:/galaxy/server/database/objects/0/b/f/dataset_0bf6ddc6-3100-41f8-97ed-17e8855f86a1_files:/galaxy/server/database/objects/0/b/f/dataset_0bf6ddc6-3100-41f8-97ed-17e8855f86a1.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:24,878 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:51:25,674 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11, 13, 10, 9, 12 +tpv.core.entities DEBUG 2024-09-12 12:51:25,758 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:25,759 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:25,766 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:25,788 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:25,815 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (9) Working directory for job is: /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:25,824 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [9] queued (58.182 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:25,829 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:25,835 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 9 +tpv.core.entities DEBUG 2024-09-12 12:51:25,850 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:25,851 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:25,859 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:25,876 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:25,910 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (10) Working directory for job is: /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:25,918 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [10] queued (58.600 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:25,922 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:25,929 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 10 +tpv.core.entities DEBUG 2024-09-12 12:51:25,949 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:25,950 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:25,959 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:25,982 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:25,991 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [9] prepared (128.016 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:26,028 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '9:/galaxy/server/database/objects/9/e/0/dataset_9e0ccf7a-a0f8-470f-a32d-49b48b63eac8_files:/galaxy/server/database/objects/9/e/0/dataset_9e0ccf7a-a0f8-470f-a32d-49b48b63eac8.dat'] +galaxy.jobs DEBUG 2024-09-12 12:51:26,029 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (11) Working directory for job is: /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,040 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [11] queued (80.996 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:26,045 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:26,051 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 11 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,089 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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" +tpv.core.entities DEBUG 2024-09-12 12:51:26,094 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:26,095 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:26,103 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:26,112 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [10] prepared (153.811 ms) +galaxy.jobs DEBUG 2024-09-12 12:51:26,132 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:26,156 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '10:/galaxy/server/database/objects/f/8/7/dataset_f87fcff8-5977-4564-bc22-3c4a1c90531c_files:/galaxy/server/database/objects/f/8/7/dataset_f87fcff8-5977-4564-bc22-3c4a1c90531c.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,179 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 DEBUG 2024-09-12 12:51:26,193 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (12) Working directory for job is: /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,203 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [12] queued (99.898 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:26,209 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:26,220 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 12 +tpv.core.entities DEBUG 2024-09-12 12:51:26,232 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:26,233 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:26,243 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:26,263 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [11] prepared (172.461 ms) +galaxy.jobs DEBUG 2024-09-12 12:51:26,266 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:26,300 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/11/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/11/registry.xml' '/galaxy/server/database/jobs_directory/000/11/upload_params.json' '11:/galaxy/server/database/objects/6/1/b/dataset_61be301a-6761-4c78-ad4a-07c493220933_files:/galaxy/server/database/objects/6/1/b/dataset_61be301a-6761-4c78-ad4a-07c493220933.dat'] +galaxy.jobs DEBUG 2024-09-12 12:51:26,305 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (13) Working directory for job is: /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,317 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [13] queued (73.390 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:26,322 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:26,330 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 13 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,348 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:51:26,384 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [12] prepared (136.269 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:26,433 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/12/registry.xml' '/galaxy/server/database/jobs_directory/000/12/upload_params.json' '12:/galaxy/server/database/objects/6/f/8/dataset_6f8f4deb-8cf0-4bd1-903f-963e6d788877_files:/galaxy/server/database/objects/6/f/8/dataset_6f8f4deb-8cf0-4bd1-903f-963e6d788877.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,451 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (12) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:51:26,500 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [13] prepared (140.125 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:26,522 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/13/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '13:/galaxy/server/database/objects/0/0/f/dataset_00f54ebd-f9d7-47aa-ada7-87512d1619b7_files:/galaxy/server/database/objects/0/0/f/dataset_00f54ebd-f9d7-47aa-ada7-87512d1619b7.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:26,541 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (13) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:51:27,328 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2024-09-12 12:51:27,377 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:27,378 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:27,384 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:27,405 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:27,425 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (14) Working directory for job is: /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:27,433 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [14] queued (49.037 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:27,441 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:51:27,444 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 14 +galaxy.jobs DEBUG 2024-09-12 12:51:27,576 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [14] prepared (104.641 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:51:27,600 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/14/registry.xml' '/galaxy/server/database/jobs_directory/000/14/upload_params.json' '14:/galaxy/server/database/objects/f/1/7/dataset_f17b3423-8625-4ab9-9072-dc69003fd35a_files:/galaxy/server/database/objects/f/1/7/dataset_f17b3423-8625-4ab9-9072-dc69003fd35a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:51:27,617 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 ERROR 2024-09-12 12:51:33,950 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (5/gxy-8nlqk) User killed running job, but error encountered during termination: Operation cannot be fulfilled on jobs.batch "gxy-8nlqk": the object has been modified; please apply your changes to the latest version and try again +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-8nlqk + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 908, in stop_job + self.__cleanup_k8s_job(k8s_job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-8nlqk": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-09-12 12:51:35,673 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 4: 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 2024-09-12 12:51:35,786 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 6: 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:51:37,061 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:51:37,089 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:51:47,774 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 6 finished +galaxy.model.metadata DEBUG 2024-09-12 12:51:47,884 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:47,903 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 4 finished +galaxy.jobs INFO 2024-09-12 12:51:47,975 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 6 in /galaxy/server/database/jobs_directory/000/6 +galaxy.model.metadata DEBUG 2024-09-12 12:51:48,010 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4 +galaxy.jobs DEBUG 2024-09-12 12:51:48,071 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 6 executed (269.879 ms) +galaxy.jobs INFO 2024-09-12 12:51:48,081 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 4 in /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs DEBUG 2024-09-12 12:51:48,138 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 4 executed (161.458 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:51:48,780 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 9: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:51:49,056 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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 2024-09-12 12:51:49,288 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 7 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:51:49,371 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2024-09-12 12:51:49,415 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.model.metadata DEBUG 2024-09-12 12:51:49,480 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.jobs INFO 2024-09-12 12:51:49,502 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs INFO 2024-09-12 12:51:49,553 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 8 in /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs DEBUG 2024-09-12 12:51:49,599 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 7 executed (227.796 ms) +galaxy.jobs DEBUG 2024-09-12 12:51:49,611 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 8 executed (208.013 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:51:49,694 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 16, 15, 17 +tpv.core.entities DEBUG 2024-09-12 12:51:49,767 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:49,767 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:49,775 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:49,797 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:49,856 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (15) Working directory for job is: /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:49,864 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [15] queued (88.056 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:49,868 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:49,886 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:49,886 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:49,891 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:49,908 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:49,960 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (16) Working directory for job is: /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:49,966 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 2024-09-12 12:51:49,984 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [16] queued (92.061 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:49,994 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 12:51:50,005 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 +tpv.core.entities DEBUG 2024-09-12 12:51:50,080 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:50,081 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:50,087 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:50,163 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:50,186 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (17) Working directory for job is: /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:50,194 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [17] queued (106.122 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:50,256 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.handler DEBUG 2024-09-12 12:51:51,260 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 21, 19, 23, 22, 20, 18 +tpv.core.entities DEBUG 2024-09-12 12:51:51,357 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:51,358 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:51,364 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:51,381 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:51,460 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (18) Working directory for job is: /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:51,468 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [18] queued (104.241 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:51,472 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:51,489 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:51,489 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:51,552 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:51,568 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:51,588 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (19) Working directory for job is: /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:51,596 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [19] queued (43.883 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:51,655 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:51,671 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:51,672 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:51,677 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:51,692 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:51,769 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (20) Working directory for job is: /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:51,952 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [20] queued (274.821 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:51,956 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:51,970 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:51,971 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:52,052 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:52,068 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:52,085 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (21) Working directory for job is: /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:52,093 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [21] queued (40.649 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:52,156 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:52,172 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:52,173 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:52,178 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:52,194 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:52,273 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (22) Working directory for job is: /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:52,280 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [22] queued (102.072 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:52,284 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:52,360 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:52,360 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:52,365 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:52,382 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:52,459 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (23) Working directory for job is: /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:52,467 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [23] queued (101.169 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:52,471 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.handler DEBUG 2024-09-12 12:51:53,475 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 24, 25, 26, 27, 28 +tpv.core.entities DEBUG 2024-09-12 12:51:53,658 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:53,659 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:53,665 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:53,685 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:53,762 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (24) Working directory for job is: /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:53,771 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [24] queued (105.415 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:53,776 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:53,793 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:53,794 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:53,853 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:53,872 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:53,891 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (25) Working directory for job is: /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:53,953 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [25] queued (99.599 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:53,958 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:53,974 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:53,975 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:53,980 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:54,053 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:54,073 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (26) Working directory for job is: /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:54,082 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [26] queued (101.355 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:54,086 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:54,165 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:54,166 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:54,173 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:54,192 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:54,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (27) Working directory for job is: /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:54,279 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [27] queued (106.157 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:54,284 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +tpv.core.entities DEBUG 2024-09-12 12:51:54,360 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:51:54,361 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:51:54,367 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:51:54,387 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:51:54,468 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (28) Working directory for job is: /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs.runners DEBUG 2024-09-12 12:51:54,478 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [28] queued (111.004 ms) +galaxy.jobs.handler INFO 2024-09-12 12:51:54,483 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 12:52:01,765 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 9 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:01,877 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.jobs INFO 2024-09-12 12:52:01,973 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 9 in /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs DEBUG 2024-09-12 12:52:02,068 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 9 executed (273.284 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:02,387 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 10 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:52:02,464 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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.model.metadata DEBUG 2024-09-12 12:52:02,557 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.jobs INFO 2024-09-12 12:52:02,607 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 10 in /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs DEBUG 2024-09-12 12:52:02,709 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 10 executed (290.871 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:03,100 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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 2024-09-12 12:52:03,152 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 12 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:03,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.jobs INFO 2024-09-12 12:52:03,385 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 12 in /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:03,398 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 11 finished +galaxy.jobs DEBUG 2024-09-12 12:52:03,508 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 12 executed (313.961 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:52:03,514 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2024-09-12 12:52:03,590 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 11 in /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:03,623 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 15 +galaxy.jobs DEBUG 2024-09-12 12:52:03,687 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 11 executed (215.245 ms) +galaxy.jobs DEBUG 2024-09-12 12:52:03,806 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [15] prepared (134.536 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:03,855 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '15:/galaxy/server/database/objects/6/9/7/dataset_69760046-0335-492a-b65b-54321c15272e_files:/galaxy/server/database/objects/6/9/7/dataset_69760046-0335-492a-b65b-54321c15272e.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:03,870 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:03,876 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 16 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:03,972 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 17 +galaxy.jobs DEBUG 2024-09-12 12:52:04,079 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [16] prepared (176.085 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:04,108 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/16/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/16/registry.xml' '/galaxy/server/database/jobs_directory/000/16/upload_params.json' '16:/galaxy/server/database/objects/4/7/6/dataset_4760f9bd-c83f-4389-8196-c50687b5ca56_files:/galaxy/server/database/objects/4/7/6/dataset_4760f9bd-c83f-4389-8196-c50687b5ca56.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:04,161 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (16) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:04,200 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [17] prepared (196.048 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:04,255 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/17/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/17/registry.xml' '/galaxy/server/database/jobs_directory/000/17/upload_params.json' '17:/galaxy/server/database/objects/f/9/5/dataset_f954535b-0713-47ac-a0ce-ce69a36c1c41_files:/galaxy/server/database/objects/f/9/5/dataset_f954535b-0713-47ac-a0ce-ce69a36c1c41.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:04,275 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 18 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:04,277 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (17) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:04,397 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 19 +galaxy.jobs DEBUG 2024-09-12 12:52:04,665 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [18] prepared (361.082 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:04,706 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/18/registry.xml' '/galaxy/server/database/jobs_directory/000/18/upload_params.json' '18:/galaxy/server/database/objects/6/1/9/dataset_619fe7ee-555d-4b33-850e-668f00ca2b4f_files:/galaxy/server/database/objects/6/1/9/dataset_619fe7ee-555d-4b33-850e-668f00ca2b4f.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:04,778 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (18) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:04,809 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [19] prepared (386.195 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:04,864 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/19/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/19/registry.xml' '/galaxy/server/database/jobs_directory/000/19/upload_params.json' '19:/galaxy/server/database/objects/3/4/4/dataset_344b1e0f-70bf-4583-a6e3-53c016ba1851_files:/galaxy/server/database/objects/3/4/4/dataset_344b1e0f-70bf-4583-a6e3-53c016ba1851.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:04,881 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (19) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:04,913 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 20 +galaxy.jobs DEBUG 2024-09-12 12:52:05,080 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [20] prepared (119.576 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:05,105 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/20/registry.xml' '/galaxy/server/database/jobs_directory/000/20/upload_params.json' '20:/galaxy/server/database/objects/5/9/d/dataset_59da9f0d-d36b-47b9-b5cc-86f9efaea5e8_files:/galaxy/server/database/objects/5/9/d/dataset_59da9f0d-d36b-47b9-b5cc-86f9efaea5e8.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:05,121 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (20) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:05,175 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 21 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:05,488 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 22 +galaxy.jobs DEBUG 2024-09-12 12:52:05,579 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [21] prepared (380.753 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:05,655 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/21/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/21/registry.xml' '/galaxy/server/database/jobs_directory/000/21/upload_params.json' '21:/galaxy/server/database/objects/0/6/0/dataset_060a2488-8d11-4af2-bfe5-171ae0eaf59a_files:/galaxy/server/database/objects/0/6/0/dataset_060a2488-8d11-4af2-bfe5-171ae0eaf59a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:05,688 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (21) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:05,897 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [22] prepared (314.639 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:05,979 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 23 +galaxy.jobs.command_factory INFO 2024-09-12 12:52:05,985 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/22/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/22/registry.xml' '/galaxy/server/database/jobs_directory/000/22/upload_params.json' '22:/galaxy/server/database/objects/b/c/3/dataset_bc3c3ec5-7d79-45f8-b4dd-5541155ed95d_files:/galaxy/server/database/objects/b/c/3/dataset_bc3c3ec5-7d79-45f8-b4dd-5541155ed95d.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:06,065 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (22) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:06,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 24 +galaxy.jobs DEBUG 2024-09-12 12:52:06,464 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [23] prepared (391.806 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:06,505 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/23/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/23/registry.xml' '/galaxy/server/database/jobs_directory/000/23/upload_params.json' '23:/galaxy/server/database/objects/2/5/9/dataset_259bac96-7e36-43c9-8aba-6baee12b3cec_files:/galaxy/server/database/objects/2/5/9/dataset_259bac96-7e36-43c9-8aba-6baee12b3cec.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:06,584 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (23) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:06,621 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [24] prepared (238.594 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:06,682 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/24/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/24/registry.xml' '/galaxy/server/database/jobs_directory/000/24/upload_params.json' '24:/galaxy/server/database/objects/8/7/e/dataset_87ecbb54-15ec-4829-bb0e-e0bc531e6b52_files:/galaxy/server/database/objects/8/7/e/dataset_87ecbb54-15ec-4829-bb0e-e0bc531e6b52.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:06,704 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (24) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:06,712 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 25 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:06,873 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 26 +galaxy.jobs DEBUG 2024-09-12 12:52:06,953 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [25] prepared (177.766 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:06,989 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/25/registry.xml' '/galaxy/server/database/jobs_directory/000/25/upload_params.json' '25:/galaxy/server/database/objects/6/8/a/dataset_68abf4f0-69dc-47eb-88ac-7ad212d0f628_files:/galaxy/server/database/objects/6/8/a/dataset_68abf4f0-69dc-47eb-88ac-7ad212d0f628.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:07,008 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (25) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:07,081 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [26] prepared (178.059 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:07,112 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/26/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/26/registry.xml' '/galaxy/server/database/jobs_directory/000/26/upload_params.json' '26:/galaxy/server/database/objects/6/4/a/dataset_64af048e-9f8f-4761-a608-a00efc2cba86_files:/galaxy/server/database/objects/6/4/a/dataset_64af048e-9f8f-4761-a608-a00efc2cba86.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:07,119 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 27 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:07,155 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (26) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:07,291 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 28 +galaxy.jobs DEBUG 2024-09-12 12:52:07,361 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [27] prepared (187.216 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:07,397 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/27/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/27/registry.xml' '/galaxy/server/database/jobs_directory/000/27/upload_params.json' '27:/galaxy/server/database/objects/8/8/4/dataset_88470fa9-8c8e-4167-ba9a-289a12b5df7d_files:/galaxy/server/database/objects/8/8/4/dataset_88470fa9-8c8e-4167-ba9a-289a12b5df7d.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:07,415 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (27) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:07,505 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [28] prepared (184.559 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:07,554 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/28/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/28/registry.xml' '/galaxy/server/database/jobs_directory/000/28/upload_params.json' '28:/galaxy/server/database/objects/f/d/1/dataset_fd1f55e3-b263-4e2e-bf0d-a08106e6cb26_files:/galaxy/server/database/objects/f/d/1/dataset_fd1f55e3-b263-4e2e-bf0d-a08106e6cb26.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:07,570 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (28) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:52:12,573 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 13 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:12,654 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.jobs INFO 2024-09-12 12:52:12,702 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 13 in /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs DEBUG 2024-09-12 12:52:12,784 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 13 executed (167.619 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:12,863 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:12,933 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.jobs INFO 2024-09-12 12:52:12,980 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs DEBUG 2024-09-12 12:52:13,035 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 14 executed (142.443 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:13,896 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 15: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:52:13,918 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:52:15,271 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:52:18,394 [pN:job_handler_0,p:9,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.kubernetes ERROR 2024-09-12 12:52:19,286 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-c68h9 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-c68h9": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-09-12 12:52:25,972 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 16 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:26,171 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 16 +galaxy.jobs INFO 2024-09-12 12:52:26,278 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 16 in /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs DEBUG 2024-09-12 12:52:26,393 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 16 executed (320.936 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:26,666 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 15 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:26,757 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:26,767 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 19: 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 INFO 2024-09-12 12:52:26,866 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 15 in /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs DEBUG 2024-09-12 12:52:26,910 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 15 executed (215.045 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:27,256 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:52:28,072 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:28,183 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.jobs INFO 2024-09-12 12:52:28,273 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2024-09-12 12:52:28,369 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 17 executed (267.279 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:28,695 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:52:31,160 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 18 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:31,274 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.jobs INFO 2024-09-12 12:52:31,364 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 18 in /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs DEBUG 2024-09-12 12:52:31,562 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 18 executed (372.016 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:31,955 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:52:39,653 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 19 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:39,756 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.jobs INFO 2024-09-12 12:52:39,800 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 19 in /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs DEBUG 2024-09-12 12:52:39,891 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 19 executed (208.915 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:40,266 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 20 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:52:40,295 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 23: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.model.metadata DEBUG 2024-09-12 12:52:40,384 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.jobs INFO 2024-09-12 12:52:40,470 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 20 in /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs DEBUG 2024-09-12 12:52:40,557 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 20 executed (265.044 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:40,899 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:52:41,469 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:41,588 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.jobs INFO 2024-09-12 12:52:41,680 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 21 in /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs DEBUG 2024-09-12 12:52:41,777 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 21 executed (275.212 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:42,000 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (25/gxy-c68h9) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-12 12:52:42,657 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 27: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:52:44,660 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 22 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:44,780 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.jobs INFO 2024-09-12 12:52:44,877 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 22 in /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs DEBUG 2024-09-12 12:52:44,968 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 22 executed (275.294 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:45,586 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:52:53,172 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 23 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:53,282 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.jobs INFO 2024-09-12 12:52:53,370 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 23 in /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs DEBUG 2024-09-12 12:52:53,469 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 23 executed (266.750 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:52:53,782 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 24 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:52:53,799 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 26: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.model.metadata DEBUG 2024-09-12 12:52:53,901 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.jobs INFO 2024-09-12 12:52:53,997 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2024-09-12 12:52:54,097 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 24 executed (235.484 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:52:54,995 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2024-09-12 12:52:55,071 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:55,072 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:55,078 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:55,096 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:55,164 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (29) Working directory for job is: /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:55,172 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [29] queued (93.620 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:55,177 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:55,182 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 29 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:55,380 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 27 finished +galaxy.jobs DEBUG 2024-09-12 12:52:55,464 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [29] prepared (260.314 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:55,488 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/29/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/29/registry.xml' '/galaxy/server/database/jobs_directory/000/29/upload_params.json' '29:/galaxy/server/database/objects/b/8/6/dataset_b8604271-de17-4052-94c2-32f8b1459355_files:/galaxy/server/database/objects/b/8/6/dataset_b8604271-de17-4052-94c2-32f8b1459355.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:55,565 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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.model.metadata DEBUG 2024-09-12 12:52:55,590 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 27 +galaxy.jobs INFO 2024-09-12 12:52:55,761 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 27 in /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs DEBUG 2024-09-12 12:52:55,882 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 27 executed (396.233 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:52:56,254 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30, 31, 32, 33 +tpv.core.entities DEBUG 2024-09-12 12:52:56,296 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:56,353 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:56,359 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:56,373 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:56,390 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (30) Working directory for job is: /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:56,398 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [30] queued (39.344 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:56,403 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:56,408 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 30 +tpv.core.entities DEBUG 2024-09-12 12:52:56,421 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:56,422 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:56,459 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:56,481 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:56,514 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (31) Working directory for job is: /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:56,555 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [31] queued (95.331 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:56,561 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:56,564 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 31 +tpv.core.entities DEBUG 2024-09-12 12:52:56,587 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:56,588 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:56,597 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:56,617 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [30] prepared (155.345 ms) +galaxy.jobs DEBUG 2024-09-12 12:52:56,659 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:56,692 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '30:/galaxy/server/database/objects/3/6/5/dataset_3656b57b-ef6a-442b-88d0-6c0439d7d8a0_files:/galaxy/server/database/objects/3/6/5/dataset_3656b57b-ef6a-442b-88d0-6c0439d7d8a0.dat'] +galaxy.jobs DEBUG 2024-09-12 12:52:56,700 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (32) Working directory for job is: /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:56,709 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [32] queued (111.678 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:56,713 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 12:52:56,715 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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" +tpv.core.entities DEBUG 2024-09-12 12:52:56,772 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:56,773 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:56,781 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:56,802 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [31] prepared (212.531 ms) +galaxy.jobs DEBUG 2024-09-12 12:52:56,806 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:56,814 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 32 +galaxy.jobs.command_factory INFO 2024-09-12 12:52:56,866 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '31:/galaxy/server/database/objects/4/4/4/dataset_4449e7a8-b766-4743-a54a-08f5653c830b_files:/galaxy/server/database/objects/4/4/4/dataset_4449e7a8-b766-4743-a54a-08f5653c830b.dat'] +galaxy.jobs DEBUG 2024-09-12 12:52:56,866 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (33) Working directory for job is: /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:56,881 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [33] queued (99.719 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:56,887 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 12:52:56,899 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:57,067 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 33 +galaxy.jobs DEBUG 2024-09-12 12:52:57,069 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [32] prepared (189.373 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:57,094 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/32/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/32/registry.xml' '/galaxy/server/database/jobs_directory/000/32/upload_params.json' '32:/galaxy/server/database/objects/d/e/1/dataset_de1656ae-b389-40d7-b021-c0671d34d9c4_files:/galaxy/server/database/objects/d/e/1/dataset_de1656ae-b389-40d7-b021-c0671d34d9c4.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:57,111 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (32) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:57,262 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [33] prepared (169.124 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:57,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/33/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/33/registry.xml' '/galaxy/server/database/jobs_directory/000/33/upload_params.json' '33:/galaxy/server/database/objects/5/3/a/dataset_53aac595-f3ee-48c6-af0d-ed959bda5156_files:/galaxy/server/database/objects/5/3/a/dataset_53aac595-f3ee-48c6-af0d-ed959bda5156.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:57,301 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (33) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 DEBUG 2024-09-12 12:52:57,603 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 28 finished +galaxy.model.metadata DEBUG 2024-09-12 12:52:57,670 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.jobs INFO 2024-09-12 12:52:57,716 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 28 in /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs DEBUG 2024-09-12 12:52:57,775 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 28 executed (142.811 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:52:57,890 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 34, 35, 36, 37 +tpv.core.entities DEBUG 2024-09-12 12:52:57,926 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:57,927 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:57,932 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:57,949 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:57,967 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (34) Working directory for job is: /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:57,977 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [34] queued (44.010 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:57,983 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:57,987 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 34 +tpv.core.entities DEBUG 2024-09-12 12:52:58,004 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:58,005 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:58,012 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:58,038 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:58,094 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (35) Working directory for job is: /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,107 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [35] queued (95.352 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:58,115 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:58,122 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 35 +tpv.core.entities DEBUG 2024-09-12 12:52:58,158 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:58,160 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:58,169 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:58,213 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:58,214 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [34] prepared (195.324 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:58,262 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '34:/galaxy/server/database/objects/0/8/0/dataset_08090aa1-b426-462f-9e03-affdae50803d_files:/galaxy/server/database/objects/0/8/0/dataset_08090aa1-b426-462f-9e03-affdae50803d.dat'] +galaxy.jobs DEBUG 2024-09-12 12:52:58,274 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (36) Working directory for job is: /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,289 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [36] queued (118.393 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:58,301 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:58,311 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 36 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,326 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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" +tpv.core.entities DEBUG 2024-09-12 12:52:58,353 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:58,354 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:58,370 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:58,405 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [35] prepared (241.241 ms) +galaxy.jobs DEBUG 2024-09-12 12:52:58,423 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:58,459 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '35:/galaxy/server/database/objects/7/0/d/dataset_70dd53e0-8366-41a8-8885-577c301d3657_files:/galaxy/server/database/objects/7/0/d/dataset_70dd53e0-8366-41a8-8885-577c301d3657.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,484 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:58,487 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (37) Working directory for job is: /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,496 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [37] queued (123.699 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:58,501 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:58,509 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 37 +galaxy.jobs DEBUG 2024-09-12 12:52:58,575 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [36] prepared (195.508 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:58,616 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/36/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/36/registry.xml' '/galaxy/server/database/jobs_directory/000/36/upload_params.json' '36:/galaxy/server/database/objects/2/7/a/dataset_27a7ec31-59c8-47e1-bcf3-7987af05698a_files:/galaxy/server/database/objects/2/7/a/dataset_27a7ec31-59c8-47e1-bcf3-7987af05698a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,637 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (36) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:52:58,691 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [37] prepared (143.834 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:52:58,716 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/37/registry.xml' '/galaxy/server/database/jobs_directory/000/37/upload_params.json' '37:/galaxy/server/database/objects/8/a/4/dataset_8a4da324-d7fc-4f8a-b745-6a63c09bf79b_files:/galaxy/server/database/objects/8/a/4/dataset_8a4da324-d7fc-4f8a-b745-6a63c09bf79b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:58,732 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (37) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:52:59,505 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 38, 39, 40, 41 +tpv.core.entities DEBUG 2024-09-12 12:52:59,560 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:59,561 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:59,571 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:59,591 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:59,621 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (38) Working directory for job is: /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:59,633 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [38] queued (61.929 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:59,640 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:59,643 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 38 +tpv.core.entities DEBUG 2024-09-12 12:52:59,666 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:59,667 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:59,679 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:59,708 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:59,758 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (39) Working directory for job is: /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs.runners DEBUG 2024-09-12 12:52:59,768 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [39] queued (88.999 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:59,776 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:59,788 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 39 +tpv.core.entities DEBUG 2024-09-12 12:52:59,827 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:59,832 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:52:59,841 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:52:59,873 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:52:59,894 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [38] prepared (206.344 ms) +galaxy.jobs DEBUG 2024-09-12 12:52:59,923 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (40) Working directory for job is: /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs.command_factory INFO 2024-09-12 12:52:59,933 [pN:job_handler_0,p:9,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' '38:/galaxy/server/database/objects/e/b/e/dataset_ebec4ff0-b47f-4a3d-89a8-f2ad210e5b47_files:/galaxy/server/database/objects/e/b/e/dataset_ebec4ff0-b47f-4a3d-89a8-f2ad210e5b47.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:52:59,936 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [40] queued (94.708 ms) +galaxy.jobs.handler INFO 2024-09-12 12:52:59,944 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:52:59,953 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 40 +tpv.core.entities DEBUG 2024-09-12 12:52:59,996 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:52:59,996 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.runners DEBUG 2024-09-12 12:52:59,998 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.handler DEBUG 2024-09-12 12:53:00,010 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:00,044 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [39] prepared (204.542 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:00,053 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:00,106 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '39:/galaxy/server/database/objects/5/1/e/dataset_51e84a7e-d6b5-42f8-8192-d82be28b24f8_files:/galaxy/server/database/objects/5/1/e/dataset_51e84a7e-d6b5-42f8-8192-d82be28b24f8.dat'] +galaxy.jobs DEBUG 2024-09-12 12:53:00,111 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (41) Working directory for job is: /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:00,127 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [41] queued (116.667 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:00,133 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 12:53:00,142 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (39) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:00,161 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 41 +galaxy.jobs DEBUG 2024-09-12 12:53:00,210 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [40] prepared (208.997 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:00,255 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/40/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/40/registry.xml' '/galaxy/server/database/jobs_directory/000/40/upload_params.json' '40:/galaxy/server/database/objects/0/d/b/dataset_0dbe1646-2273-44d4-928f-a56ff4515a5e_files:/galaxy/server/database/objects/0/d/b/dataset_0dbe1646-2273-44d4-928f-a56ff4515a5e.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:00,280 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (40) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:53:00,340 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [41] prepared (140.788 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:00,366 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/41/registry.xml' '/galaxy/server/database/jobs_directory/000/41/upload_params.json' '41:/galaxy/server/database/objects/e/5/5/dataset_e55f8496-ec3c-4b67-9df7-a7404d80d303_files:/galaxy/server/database/objects/e/5/5/dataset_e55f8496-ec3c-4b67-9df7-a7404d80d303.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:00,384 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (41) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:53:01,138 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 42, 43, 44, 45, 46 +tpv.core.entities DEBUG 2024-09-12 12:53:01,200 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:01,201 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:01,214 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:01,242 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:01,268 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (42) Working directory for job is: /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,279 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [42] queued (64.506 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:01,287 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:01,293 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 42 +tpv.core.entities DEBUG 2024-09-12 12:53:01,318 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:01,318 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:01,329 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:01,363 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:01,424 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (43) Working directory for job is: /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,434 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [43] queued (105.165 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:01,440 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:01,450 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 43 +tpv.core.entities DEBUG 2024-09-12 12:53:01,477 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:01,478 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:01,486 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:01,510 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:01,521 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [42] prepared (183.259 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:01,566 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (44) Working directory for job is: /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,576 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [44] queued (90.277 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:01,586 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.command_factory INFO 2024-09-12 12:53:01,586 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '42:/galaxy/server/database/objects/3/f/6/dataset_3f6a321d-6292-4b4b-8dc6-85e0ecdf72db_files:/galaxy/server/database/objects/3/f/6/dataset_3f6a321d-6292-4b4b-8dc6-85e0ecdf72db.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:01,590 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 44 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,618 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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" +tpv.core.entities DEBUG 2024-09-12 12:53:01,630 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:01,631 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:01,640 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:01,696 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:01,700 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [43] prepared (207.135 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:01,754 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (45) Working directory for job is: /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs.command_factory INFO 2024-09-12 12:53:01,754 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/43/registry.xml' '/galaxy/server/database/jobs_directory/000/43/upload_params.json' '43:/galaxy/server/database/objects/1/b/f/dataset_1bf4c8e6-56d2-4aa1-bea2-3ae70e623bfd_files:/galaxy/server/database/objects/1/b/f/dataset_1bf4c8e6-56d2-4aa1-bea2-3ae70e623bfd.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,767 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [45] queued (127.017 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:01,774 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:01,782 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 45 +tpv.core.entities DEBUG 2024-09-12 12:53:01,805 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:01,806 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,815 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.handler DEBUG 2024-09-12 12:53:01,818 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:01,864 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:01,866 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [44] prepared (223.248 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:01,916 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/44/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/44/registry.xml' '/galaxy/server/database/jobs_directory/000/44/upload_params.json' '44:/galaxy/server/database/objects/a/0/7/dataset_a07cc6e5-8fa9-407f-b520-28ee67aa8d68_files:/galaxy/server/database/objects/a/0/7/dataset_a07cc6e5-8fa9-407f-b520-28ee67aa8d68.dat'] +galaxy.jobs DEBUG 2024-09-12 12:53:01,930 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (46) Working directory for job is: /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,940 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (44) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:53:01,942 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [46] queued (122.123 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:01,947 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs DEBUG 2024-09-12 12:53:02,014 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [45] prepared (183.485 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:02,037 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/45/registry.xml' '/galaxy/server/database/jobs_directory/000/45/upload_params.json' '45:/galaxy/server/database/objects/9/c/b/dataset_9cb7998d-dfba-476b-b641-0b3b1bd61ca3_files:/galaxy/server/database/objects/9/c/b/dataset_9cb7998d-dfba-476b-b641-0b3b1bd61ca3.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:02,060 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (45) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:02,063 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 46 +galaxy.jobs DEBUG 2024-09-12 12:53:02,232 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [46] prepared (132.353 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:02,267 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/46/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/46/registry.xml' '/galaxy/server/database/jobs_directory/000/46/upload_params.json' '46:/galaxy/server/database/objects/7/4/3/dataset_7436b02f-96cc-4612-8b20-473ed31cc39b_files:/galaxy/server/database/objects/7/4/3/dataset_7436b02f-96cc-4612-8b20-473ed31cc39b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:02,290 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (46) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.runners DEBUG 2024-09-12 12:53:02,944 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 26 finished +galaxy.jobs.handler DEBUG 2024-09-12 12:53:02,953 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 47, 48, 49, 50, 51 +tpv.core.entities DEBUG 2024-09-12 12:53:03,034 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:03,034 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:03,046 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:03,083 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.model.metadata DEBUG 2024-09-12 12:53:03,097 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 26 +galaxy.jobs DEBUG 2024-09-12 12:53:03,115 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (47) Working directory for job is: /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,126 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [47] queued (79.669 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:03,132 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:03,143 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 47 +tpv.core.entities DEBUG 2024-09-12 12:53:03,172 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:03,172 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:03,183 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs INFO 2024-09-12 12:53:03,183 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 26 in /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs DEBUG 2024-09-12 12:53:03,215 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:03,261 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (48) Working directory for job is: /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [48] queued (85.663 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:03,275 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:03,286 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 48 +tpv.core.entities DEBUG 2024-09-12 12:53:03,307 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:03,308 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:03,319 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:03,349 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:03,379 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [47] prepared (195.478 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:03,392 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 26 executed (374.196 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:03,408 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (49) Working directory for job is: /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,430 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [49] queued (111.396 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:03,442 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '47:/galaxy/server/database/objects/3/9/e/dataset_39e66775-1453-4a34-a55e-b0ce5fdf193c_files:/galaxy/server/database/objects/3/9/e/dataset_39e66775-1453-4a34-a55e-b0ce5fdf193c.dat'] +galaxy.jobs.handler INFO 2024-09-12 12:53:03,445 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:03,448 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 49 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,475 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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" +tpv.core.entities DEBUG 2024-09-12 12:53:03,505 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:03,506 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:03,520 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:03,560 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:03,574 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [48] prepared (238.626 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:03,623 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (50) Working directory for job is: /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs.command_factory INFO 2024-09-12 12:53:03,631 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/48/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/48/registry.xml' '/galaxy/server/database/jobs_directory/000/48/upload_params.json' '48:/galaxy/server/database/objects/a/f/3/dataset_af36a31c-6526-433b-ad05-c1bb1820e175_files:/galaxy/server/database/objects/a/f/3/dataset_af36a31c-6526-433b-ad05-c1bb1820e175.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,639 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [50] queued (118.707 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:03,656 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:03,659 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 50 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,676 [pN:job_handler_0,p:9,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" +tpv.core.entities DEBUG 2024-09-12 12:53:03,703 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:03,704 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:03,715 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:03,737 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [49] prepared (237.517 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:03,754 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:03,796 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '49:/galaxy/server/database/objects/8/a/1/dataset_8a1282f2-88ee-44db-b466-1be1dbe7212d_files:/galaxy/server/database/objects/8/a/1/dataset_8a1282f2-88ee-44db-b466-1be1dbe7212d.dat'] +galaxy.jobs DEBUG 2024-09-12 12:53:03,808 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (51) Working directory for job is: /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,820 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,822 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [51] queued (106.468 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:03,834 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:03,836 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 51 +galaxy.jobs DEBUG 2024-09-12 12:53:03,921 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [50] prepared (219.860 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:03,966 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/50/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/50/registry.xml' '/galaxy/server/database/jobs_directory/000/50/upload_params.json' '50:/galaxy/server/database/objects/5/4/f/dataset_54f53886-1c22-4dbc-b0bd-6049efacf705_files:/galaxy/server/database/objects/5/4/f/dataset_54f53886-1c22-4dbc-b0bd-6049efacf705.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:03,994 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (50) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:53:04,044 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [51] prepared (165.868 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:04,070 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/51/registry.xml' '/galaxy/server/database/jobs_directory/000/51/upload_params.json' '51:/galaxy/server/database/objects/a/5/5/dataset_a5546993-87a8-4bda-92db-32150f5074d0_files:/galaxy/server/database/objects/a/5/5/dataset_a5546993-87a8-4bda-92db-32150f5074d0.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:04,089 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (51) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:53:04,840 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52, 53, 54, 55, 56 +tpv.core.entities DEBUG 2024-09-12 12:53:04,895 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:04,896 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:04,904 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:04,932 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:04,961 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (52) Working directory for job is: /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:04,970 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [52] queued (65.844 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:04,977 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:04,982 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 52 +tpv.core.entities DEBUG 2024-09-12 12:53:05,004 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:05,005 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:05,013 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:05,040 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:05,098 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (53) Working directory for job is: /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,110 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [53] queued (96.209 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:05,119 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:05,127 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 53 +galaxy.jobs DEBUG 2024-09-12 12:53:05,166 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [52] prepared (152.880 ms) +tpv.core.entities DEBUG 2024-09-12 12:53:05,172 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:05,173 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:05,182 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs.command_factory INFO 2024-09-12 12:53:05,204 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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' '52:/galaxy/server/database/objects/c/2/f/dataset_c2f626ac-9d0b-4d0c-8fde-356de951875f_files:/galaxy/server/database/objects/c/2/f/dataset_c2f626ac-9d0b-4d0c-8fde-356de951875f.dat'] +galaxy.jobs DEBUG 2024-09-12 12:53:05,211 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,256 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 2024-09-12 12:53:05,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (54) Working directory for job is: /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,282 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [54] queued (99.844 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:05,294 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:05,306 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 54 +tpv.core.entities DEBUG 2024-09-12 12:53:05,335 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:05,336 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:05,351 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:05,378 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [53] prepared (202.833 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:05,384 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:05,459 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '53:/galaxy/server/database/objects/4/b/4/dataset_4b469942-d047-40c5-a0c4-d92a2b3aa12e_files:/galaxy/server/database/objects/4/b/4/dataset_4b469942-d047-40c5-a0c4-d92a2b3aa12e.dat'] +galaxy.jobs DEBUG 2024-09-12 12:53:05,482 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (55) Working directory for job is: /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,493 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [55] queued (141.723 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,499 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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.handler INFO 2024-09-12 12:53:05,501 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:05,509 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 55 +tpv.core.entities DEBUG 2024-09-12 12:53:05,583 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:05,583 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:05,598 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:05,670 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [54] prepared (310.280 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:05,677 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:05,768 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '54:/galaxy/server/database/objects/b/4/b/dataset_b4b0ca55-1bed-45bb-a46d-d4e3624b34d5_files:/galaxy/server/database/objects/b/4/b/dataset_b4b0ca55-1bed-45bb-a46d-d4e3624b34d5.dat'] +galaxy.jobs DEBUG 2024-09-12 12:53:05,788 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (56) Working directory for job is: /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,795 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,803 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [56] queued (204.454 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:05,808 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:05,818 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 56 +galaxy.jobs DEBUG 2024-09-12 12:53:05,883 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [55] prepared (287.436 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:05,911 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/55/registry.xml' '/galaxy/server/database/jobs_directory/000/55/upload_params.json' '55:/galaxy/server/database/objects/e/4/8/dataset_e483169f-ca43-42cc-bb4f-c42e13228f70_files:/galaxy/server/database/objects/e/4/8/dataset_e483169f-ca43-42cc-bb4f-c42e13228f70.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:05,986 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (55) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:53:06,112 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [56] prepared (220.734 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:06,143 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/56/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/56/registry.xml' '/galaxy/server/database/jobs_directory/000/56/upload_params.json' '56:/galaxy/server/database/objects/f/8/b/dataset_f8b985a0-241b-4d4a-89b4-13b30767295d_files:/galaxy/server/database/objects/f/8/b/dataset_f8b985a0-241b-4d4a-89b4-13b30767295d.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:06,162 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (56) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.runners.kubernetes ERROR 2024-09-12 12:53:06,291 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-4xszk + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-4xszk": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:06,630 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (29/gxy-4xszk) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-12 12:53:06,812 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 58, 57 +tpv.core.entities DEBUG 2024-09-12 12:53:06,876 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:06,876 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:06,883 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:06,910 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:06,937 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (57) Working directory for job is: /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:06,950 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [57] queued (66.134 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:06,955 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:06,963 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 57 +tpv.core.entities DEBUG 2024-09-12 12:53:06,979 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:06,980 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:06,989 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:07,022 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:07,071 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (58) Working directory for job is: /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:07,084 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [58] queued (94.569 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:07,095 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:07,102 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 58 +galaxy.jobs DEBUG 2024-09-12 12:53:07,164 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [57] prepared (169.369 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:07,212 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '57:/galaxy/server/database/objects/4/b/5/dataset_4b5427e3-a47a-43d2-a11e-582cd4c7dcba_files:/galaxy/server/database/objects/4/b/5/dataset_4b5427e3-a47a-43d2-a11e-582cd4c7dcba.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:07,229 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:53:07,323 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [58] prepared (183.668 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:07,369 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/58/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/58/registry.xml' '/galaxy/server/database/jobs_directory/000/58/upload_params.json' '58:/galaxy/server/database/objects/4/c/c/dataset_4cc21d85-6f8d-4bb5-a7fc-085051208a7c_files:/galaxy/server/database/objects/4/c/c/dataset_4cc21d85-6f8d-4bb5-a7fc-085051208a7c.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:07,387 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (58) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:53:08,099 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60, 59 +tpv.core.entities DEBUG 2024-09-12 12:53:08,147 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:08,148 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:08,155 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:08,176 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:08,198 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (59) Working directory for job is: /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:08,207 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [59] queued (51.469 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:08,212 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:08,218 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 59 +tpv.core.entities DEBUG 2024-09-12 12:53:08,233 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:53:08,233 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:53:08,240 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:53:08,259 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:53:08,298 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (60) Working directory for job is: /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:08,307 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [60] queued (66.957 ms) +galaxy.jobs.handler INFO 2024-09-12 12:53:08,313 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:08,316 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 60 +galaxy.jobs DEBUG 2024-09-12 12:53:08,373 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [59] prepared (128.776 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:08,410 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/59/registry.xml' '/galaxy/server/database/jobs_directory/000/59/upload_params.json' '59:/galaxy/server/database/objects/2/4/f/dataset_24f805b6-5b52-4e20-a439-529a0449687b_files:/galaxy/server/database/objects/2/4/f/dataset_24f805b6-5b52-4e20-a439-529a0449687b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:08,429 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:53:08,473 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [60] prepared (129.490 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:53:08,499 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '60:/galaxy/server/database/objects/f/d/b/dataset_fdb968eb-e622-496d-ad5f-06d9bab16eff_files:/galaxy/server/database/objects/f/d/b/dataset_fdb968eb-e622-496d-ad5f-06d9bab16eff.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:53:08,517 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (60) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:53:09,238 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 30: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:53:09,282 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:53:09,378 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:53:09,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 ERROR 2024-09-12 12:53:14,295 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-jd4k2 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-jd4k2": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-09-12 12:53:26,579 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 32 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:53:26,683 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2024-09-12 12:53:26,708 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.model.metadata DEBUG 2024-09-12 12:53:26,810 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.jobs INFO 2024-09-12 12:53:26,813 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 32 in /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:26,886 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 31 finished +galaxy.jobs INFO 2024-09-12 12:53:26,896 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2024-09-12 12:53:26,927 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 32 executed (271.331 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:26,939 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 30 finished +galaxy.model.metadata DEBUG 2024-09-12 12:53:26,982 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.jobs DEBUG 2024-09-12 12:53:27,023 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 33 executed (259.462 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:53:27,090 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.jobs INFO 2024-09-12 12:53:27,091 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 31 in /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs INFO 2024-09-12 12:53:27,154 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 30 in /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs DEBUG 2024-09-12 12:53:27,211 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 31 executed (295.515 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:27,245 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 30 executed (241.144 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:27,274 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 12:53:27,336 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:53:27,560 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 36: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:53:27,590 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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.kubernetes ERROR 2024-09-12 12:53:30,385 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-gfx5m + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-gfx5m": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-09-12 12:53:40,281 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 34 finished +galaxy.model.metadata DEBUG 2024-09-12 12:53:40,393 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.jobs INFO 2024-09-12 12:53:40,479 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 34 in /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs DEBUG 2024-09-12 12:53:40,565 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 34 executed (208.248 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:40,769 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 35 finished +galaxy.model.metadata DEBUG 2024-09-12 12:53:40,874 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.jobs INFO 2024-09-12 12:53:40,920 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 35 in /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:40,959 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 DEBUG 2024-09-12 12:53:40,997 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 36 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:53:41,054 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 37 finished +galaxy.jobs DEBUG 2024-09-12 12:53:41,090 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 35 executed (292.050 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:53:41,126 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.model.metadata DEBUG 2024-09-12 12:53:41,150 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.jobs INFO 2024-09-12 12:53:41,196 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs INFO 2024-09-12 12:53:41,209 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 37 in /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs DEBUG 2024-09-12 12:53:41,265 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 36 executed (193.576 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:41,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 37 executed (190.470 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:41,333 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:53:41,557 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:53:41,672 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 2024-09-12 12:53:53,891 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2024-09-12 12:53:54,056 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.jobs INFO 2024-09-12 12:53:54,152 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs DEBUG 2024-09-12 12:53:54,207 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 38 executed (233.066 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:54,368 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 39 finished +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:53:54,413 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (42/gxy-jd4k2) Terminated at user's request +galaxy.model.metadata DEBUG 2024-09-12 12:53:54,479 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.jobs INFO 2024-09-12 12:53:54,579 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2024-09-12 12:53:54,673 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 39 executed (276.665 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:54,727 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 41 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:53:54,760 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2024-09-12 12:53:54,842 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 41 +galaxy.model.metadata DEBUG 2024-09-12 12:53:54,843 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:54,896 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 INFO 2024-09-12 12:53:54,923 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 41 in /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs INFO 2024-09-12 12:53:54,935 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 40 in /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs.runners DEBUG 2024-09-12 12:53:54,968 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs DEBUG 2024-09-12 12:53:54,999 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 41 executed (208.677 ms) +galaxy.jobs DEBUG 2024-09-12 12:53:55,023 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 40 executed (229.904 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:53:55,304 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 55: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:53:55,364 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:54:08,176 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:08,286 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.jobs INFO 2024-09-12 12:54:08,370 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 43 in /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:08,394 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 44 finished +galaxy.jobs DEBUG 2024-09-12 12:54:08,489 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 43 executed (285.522 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:54:08,519 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.jobs INFO 2024-09-12 12:54:08,601 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2024-09-12 12:54:08,693 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 44 executed (224.617 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:08,782 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 46 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:54:08,785 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:54:08,800 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 55 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:08,897 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.model.metadata DEBUG 2024-09-12 12:54:08,901 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.jobs INFO 2024-09-12 12:54:08,958 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 46 in /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs INFO 2024-09-12 12:54:08,965 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 55 in /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:09,004 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs DEBUG 2024-09-12 12:54:09,034 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 46 executed (193.988 ms) +galaxy.jobs DEBUG 2024-09-12 12:54:09,036 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 55 executed (179.539 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:09,356 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:54:09,371 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 DEBUG 2024-09-12 12:54:21,879 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 58 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:54:21,959 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 45 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:22,001 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.model.metadata DEBUG 2024-09-12 12:54:22,073 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.jobs INFO 2024-09-12 12:54:22,093 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 58 in /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs INFO 2024-09-12 12:54:22,155 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs DEBUG 2024-09-12 12:54:22,188 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 58 executed (229.910 ms) +galaxy.jobs DEBUG 2024-09-12 12:54:22,219 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 45 executed (227.265 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:22,322 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 60 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:54:22,427 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:22,441 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.jobs INFO 2024-09-12 12:54:22,498 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:22,510 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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.model.metadata DEBUG 2024-09-12 12:54:22,549 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs INFO 2024-09-12 12:54:22,601 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:22,604 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs DEBUG 2024-09-12 12:54:22,637 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 60 executed (246.503 ms) +galaxy.jobs DEBUG 2024-09-12 12:54:22,697 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 59 executed (222.445 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:22,955 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:54:23,058 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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.handler DEBUG 2024-09-12 12:54:23,292 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2024-09-12 12:54:23,458 [pN:job_handler_0,p:9,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={'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/multiqc/multiqc/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:54:23,459 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:54:23,466 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:54:23,490 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:54:23,569 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (61) Working directory for job is: /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:23,582 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [61] queued (115.645 ms) +galaxy.jobs.handler INFO 2024-09-12 12:54:23,586 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 12:54:36,053 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 56 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:36,260 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.jobs INFO 2024-09-12 12:54:36,382 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:36,393 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 54 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:54:36,466 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 57 finished +galaxy.jobs DEBUG 2024-09-12 12:54:36,525 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 56 executed (439.821 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:54:36,536 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.model.metadata DEBUG 2024-09-12 12:54:36,565 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.jobs INFO 2024-09-12 12:54:36,612 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 54 in /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:36,618 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 47 finished +galaxy.jobs INFO 2024-09-12 12:54:36,634 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 57 in /galaxy/server/database/jobs_directory/000/57 +galaxy.model.metadata DEBUG 2024-09-12 12:54:36,705 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.jobs DEBUG 2024-09-12 12:54:36,725 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 54 executed (242.933 ms) +galaxy.jobs DEBUG 2024-09-12 12:54:36,737 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 57 executed (234.729 ms) +galaxy.jobs INFO 2024-09-12 12:54:36,762 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 47 in /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs.runners DEBUG 2024-09-12 12:54:36,826 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 DEBUG 2024-09-12 12:54:36,872 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 47 executed (210.966 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:37,045 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:54:37,070 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.kubernetes DEBUG 2024-09-12 12:54:37,086 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (51/gxy-gfx5m) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-12 12:54:37,591 [pN:job_handler_0,p:9,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 2024-09-12 12:54:49,963 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 48 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:50,078 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.jobs INFO 2024-09-12 12:54:50,166 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs DEBUG 2024-09-12 12:54:50,263 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 48 executed (271.837 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:50,267 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 49 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:54:50,380 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 50 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:50,385 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.jobs INFO 2024-09-12 12:54:50,459 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 49 in /galaxy/server/database/jobs_directory/000/49 +galaxy.model.metadata DEBUG 2024-09-12 12:54:50,483 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.jobs INFO 2024-09-12 12:54:50,525 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 50 in /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs DEBUG 2024-09-12 12:54:50,542 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 49 executed (238.106 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:50,562 [pN:job_handler_0,p:9,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 2024-09-12 12:54:50,612 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 61 +galaxy.jobs DEBUG 2024-09-12 12:54:50,613 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 50 executed (194.102 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:54:50,657 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 52 finished +galaxy.security.object_wrapper WARNING 2024-09-12 12:54:50,754 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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() +galaxy.model.metadata DEBUG 2024-09-12 12:54:50,758 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.jobs INFO 2024-09-12 12:54:51,070 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 52 in /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs DEBUG 2024-09-12 12:54:51,253 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [61] prepared (596.606 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:54:51,253 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:54:51,254 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1: multiqc:1.9 +galaxy.jobs DEBUG 2024-09-12 12:54:51,281 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 52 executed (580.149 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:54:51,512 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/multiqc:1.9--py_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:54:51,538 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [multiqc --version > /galaxy/server/database/jobs_directory/000/61/outputs/COMMAND_VERSION 2>&1; +die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/custom_content_0 && ln -s '/galaxy/server/database/objects/2/4/f/dataset_24f805b6-5b52-4e20-a439-529a0449687b.dat' 'multiqc_WDir/custom_content_0/file_0_0' && more /galaxy/server/database/objects/2/4/f/dataset_24f805b6-5b52-4e20-a439-529a0449687b.dat && ln -s '/galaxy/server/database/objects/f/d/b/dataset_fdb968eb-e622-496d-ad5f-06d9bab16eff.dat' 'multiqc_WDir/custom_content_0/file_0_1' && more /galaxy/server/database/objects/f/d/b/dataset_fdb968eb-e622-496d-ad5f-06d9bab16eff.dat && multiqc multiqc_WDir --filename "report" --config '/galaxy/server/database/jobs_directory/000/61/configs/tmpy7npc9fe'] +galaxy.jobs.runners DEBUG 2024-09-12 12:54:51,554 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (61) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/61/working/report.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/61/working/report.html" "/galaxy/server/database/objects/4/c/8/dataset_4c850119-0ad5-43ba-a065-19942a8a5841.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:54:51,567 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:54:51,567 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1: multiqc:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:54:51,589 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/multiqc:1.9--py_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:54:56,980 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 53 finished +galaxy.model.metadata DEBUG 2024-09-12 12:54:57,044 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.jobs INFO 2024-09-12 12:54:57,084 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 53 in /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs DEBUG 2024-09-12 12:54:57,141 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 53 executed (134.063 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:55:11,529 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 61: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:55:17,835 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 61 finished +galaxy.model.store.discover DEBUG 2024-09-12 12:55:17,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (61) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/61/working/report_data/multiqc_sources.txt] with element identifier [sources] for output [stats] (7.593 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:55:17,927 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (61) Add dynamic collection datasets to history for output [stats] (17.422 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:55:17,946 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.jobs INFO 2024-09-12 12:55:18,004 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 61 in /galaxy/server/database/jobs_directory/000/61 +galaxy.objectstore CRITICAL 2024-09-12 12:55:18,045 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'multiqc.log' +galaxy.jobs DEBUG 2024-09-12 12:55:18,045 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 61 executed (173.051 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:55:20,121 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62, 63 +tpv.core.entities DEBUG 2024-09-12 12:55:20,162 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:55:20,163 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:55:20,169 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:55:20,185 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:55:20,203 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (62) Working directory for job is: /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs.runners DEBUG 2024-09-12 12:55:20,211 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [62] queued (42.085 ms) +galaxy.jobs.handler INFO 2024-09-12 12:55:20,215 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:55:20,221 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 62 +tpv.core.entities DEBUG 2024-09-12 12:55:20,233 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:55:20,234 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:55:20,241 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:55:20,260 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:55:20,296 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (63) Working directory for job is: /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs.runners DEBUG 2024-09-12 12:55:20,306 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [63] queued (64.743 ms) +galaxy.jobs.handler INFO 2024-09-12 12:55:20,310 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:55:20,316 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 63 +galaxy.jobs DEBUG 2024-09-12 12:55:20,353 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [62] prepared (107.845 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:55:20,387 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/62/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/62/registry.xml' '/galaxy/server/database/jobs_directory/000/62/upload_params.json' '63:/galaxy/server/database/objects/6/a/e/dataset_6ae365f2-fa59-4bfa-8285-e06f53c2ef2f_files:/galaxy/server/database/objects/6/a/e/dataset_6ae365f2-fa59-4bfa-8285-e06f53c2ef2f.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:55:20,401 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:55:20,437 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [63] prepared (100.635 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:55:20,462 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/63/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/63/registry.xml' '/galaxy/server/database/jobs_directory/000/63/upload_params.json' '64:/galaxy/server/database/objects/d/d/1/dataset_dd1ee562-0bfe-4280-b4b3-307414b8c412_files:/galaxy/server/database/objects/d/d/1/dataset_dd1ee562-0bfe-4280-b4b3-307414b8c412.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:55:20,476 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (63) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:55:29,893 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 62: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:55:30,930 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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 2024-09-12 12:55:36,715 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 62 finished +galaxy.model.metadata DEBUG 2024-09-12 12:55:36,780 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2024-09-12 12:55:36,839 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 62 in /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs DEBUG 2024-09-12 12:55:36,887 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 62 executed (141.507 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:55:37,619 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2024-09-12 12:55:37,678 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.jobs INFO 2024-09-12 12:55:37,714 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 63 in /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs DEBUG 2024-09-12 12:55:37,757 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 63 executed (109.606 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:55:38,846 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64 +tpv.core.entities DEBUG 2024-09-12 12:55:38,887 [pN:job_handler_0,p:9,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={'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/multiqc/multiqc/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:55:38,888 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:55:38,893 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:55:38,910 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:55:38,926 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (64) Working directory for job is: /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs.runners DEBUG 2024-09-12 12:55:38,935 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [64] queued (41.652 ms) +galaxy.jobs.handler INFO 2024-09-12 12:55:38,939 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:55:38,943 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 64 +galaxy.jobs DEBUG 2024-09-12 12:55:39,042 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [64] prepared (79.623 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:55:39,043 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:55:39,043 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1: multiqc:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:55:39,067 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/multiqc:1.9--py_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:55:39,091 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/64/tool_script.sh] for tool command [multiqc --version > /galaxy/server/database/jobs_directory/000/64/outputs/COMMAND_VERSION 2>&1; +die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastqc_0 && mkdir 'multiqc_WDir/fastqc_0/data_0' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/galaxy/server/database/objects/6/a/e/dataset_6ae365f2-fa59-4bfa-8285-e06f53c2ef2f.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/galaxy/server/database/objects/d/d/1/dataset_dd1ee562-0bfe-4280-b4b3-307414b8c412.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' && multiqc multiqc_WDir --filename "report" --title "Title of the report" --comment "Commment for the report" --flat --export] +galaxy.jobs.runners DEBUG 2024-09-12 12:55:39,106 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/64/working/report.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/64/working/report.html" "/galaxy/server/database/objects/a/a/2/dataset_aa2f20a8-f2c3-4309-8fe6-5d159c76ea1c.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:55:39,117 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:55:39,118 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1: multiqc:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:55:39,138 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/multiqc:1.9--py_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:55:55,274 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:56:01,548 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 64 finished +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,622 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_per_base_n_content_plot_1.txt] with element identifier [fastqc_per_base_n_content_plot_1] for output [plots] (7.680 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,623 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt] with element identifier [fastqc_per_base_sequence_quality_plot_1] for output [plots] (0.875 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,624 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt] with element identifier [fastqc_per_sequence_gc_content_plot_Counts] for output [plots] (0.636 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,624 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt] with element identifier [fastqc_per_sequence_gc_content_plot_Percentages] for output [plots] (0.587 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,625 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt] with element identifier [fastqc_per_sequence_quality_scores_plot_1] for output [plots] (0.569 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,626 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_sequence_counts_plot_1.txt] with element identifier [fastqc_sequence_counts_plot_1] for output [plots] (0.789 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,626 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt] with element identifier [fastqc_sequence_duplication_levels_plot_1] for output [plots] (0.570 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,700 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Add dynamic collection datasets to history for output [plots] (72.719 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,754 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/multiqc_fastqc.txt] with element identifier [fastqc] for output [stats] (1.009 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,755 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/multiqc_general_stats.txt] with element identifier [general_stats] for output [stats] (0.831 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,756 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/64/working/report_data/multiqc_sources.txt] with element identifier [sources] for output [stats] (0.651 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:01,792 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (64) Add dynamic collection datasets to history for output [stats] (36.167 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:56:01,823 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2024-09-12 12:56:01,900 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 64 in /galaxy/server/database/jobs_directory/000/64 +galaxy.objectstore CRITICAL 2024-09-12 12:56:01,934 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'mqc_fastqc_sequence_duplication_levels_plot_1.txt' +galaxy.jobs DEBUG 2024-09-12 12:56:01,934 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 64 executed (354.902 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:56:03,552 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2024-09-12 12:56:03,593 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:56:03,593 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:56:03,600 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:56:03,618 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:56:03,636 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (65) Working directory for job is: /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs.runners DEBUG 2024-09-12 12:56:03,644 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [65] queued (44.107 ms) +galaxy.jobs.handler INFO 2024-09-12 12:56:03,650 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:56:03,652 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 65 +galaxy.jobs DEBUG 2024-09-12 12:56:03,771 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [65] prepared (97.458 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:56:03,794 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/65/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/65/registry.xml' '/galaxy/server/database/jobs_directory/000/65/upload_params.json' '76:/galaxy/server/database/objects/9/8/3/dataset_9830ce18-7560-4f15-a2e5-1bdc1196173b_files:/galaxy/server/database/objects/9/8/3/dataset_9830ce18-7560-4f15-a2e5-1bdc1196173b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:56:03,809 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:56:13,611 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:56:20,040 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2024-09-12 12:56:20,108 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 76 +galaxy.jobs INFO 2024-09-12 12:56:20,148 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 65 in /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs DEBUG 2024-09-12 12:56:20,204 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 65 executed (135.307 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:56:21,194 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 66 +tpv.core.entities DEBUG 2024-09-12 12:56:21,239 [pN:job_handler_0,p:9,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={'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/multiqc/multiqc/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:56:21,240 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:56:21,246 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:56:21,265 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:56:21,286 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (66) Working directory for job is: /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs.runners DEBUG 2024-09-12 12:56:21,296 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [66] queued (49.960 ms) +galaxy.jobs.handler INFO 2024-09-12 12:56:21,301 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:56:21,306 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 66 +galaxy.jobs DEBUG 2024-09-12 12:56:21,406 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [66] prepared (78.403 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:21,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:56:21,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1: multiqc:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:21,641 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/multiqc:1.9--py_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:56:21,665 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/66/tool_script.sh] for tool command [multiqc --version > /galaxy/server/database/jobs_directory/000/66/outputs/COMMAND_VERSION 2>&1; +die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/pycoqc_0 && grep -q '"pycoqc":' /galaxy/server/database/objects/9/8/3/dataset_9830ce18-7560-4f15-a2e5-1bdc1196173b.dat || die "Module 'pycoqc: '"pycoqc":' not found in the file 'pycoqc_json'" && ln -s '/galaxy/server/database/objects/9/8/3/dataset_9830ce18-7560-4f15-a2e5-1bdc1196173b.dat' 'multiqc_WDir/pycoqc_0/pycoqc_json' && multiqc multiqc_WDir --filename "report" --title "Title of the report" --comment "Commment for the report"] +galaxy.jobs.runners DEBUG 2024-09-12 12:56:21,683 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (66) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/66/working/report.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/66/working/report.html" "/galaxy/server/database/objects/c/c/0/dataset_cc0828f6-4895-4503-a2f4-f99c8168bf48.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:21,696 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:56:21,696 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1: multiqc:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:21,720 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/multiqc:1.9--py_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:56:30,820 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:56:37,019 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 66 finished +galaxy.model.store.discover DEBUG 2024-09-12 12:56:37,091 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (66) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/66/working/report_data/multiqc_general_stats.txt] with element identifier [general_stats] for output [stats] (5.996 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:37,092 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (66) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/66/working/report_data/multiqc_sources.txt] with element identifier [sources] for output [stats] (0.845 ms) +galaxy.model.store.discover DEBUG 2024-09-12 12:56:37,120 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (66) Add dynamic collection datasets to history for output [stats] (28.260 ms) +galaxy.model.metadata DEBUG 2024-09-12 12:56:37,144 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 77 +galaxy.jobs INFO 2024-09-12 12:56:37,200 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.objectstore CRITICAL 2024-09-12 12:56:37,236 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'multiqc.log' +galaxy.jobs DEBUG 2024-09-12 12:56:37,236 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 66 executed (185.509 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:56:39,761 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67 +tpv.core.entities DEBUG 2024-09-12 12:56:39,800 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:56:39,800 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:56:39,806 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:56:39,825 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:56:39,845 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (67) Working directory for job is: /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs.runners DEBUG 2024-09-12 12:56:39,853 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [67] queued (46.530 ms) +galaxy.jobs.handler INFO 2024-09-12 12:56:39,857 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:56:39,862 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 67 +galaxy.jobs DEBUG 2024-09-12 12:56:39,969 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [67] prepared (87.067 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:56:39,991 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '80:/galaxy/server/database/objects/3/6/4/dataset_364f00e5-5045-4dcc-898d-0a5dd2b615fe_files:/galaxy/server/database/objects/3/6/4/dataset_364f00e5-5045-4dcc-898d-0a5dd2b615fe.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:56:40,006 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:56:50,122 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:56:56,567 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 67 finished +galaxy.model.metadata DEBUG 2024-09-12 12:56:56,629 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 80 +galaxy.jobs INFO 2024-09-12 12:56:56,728 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 67 in /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs DEBUG 2024-09-12 12:56:56,778 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 67 executed (182.086 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:56:57,291 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 68 +tpv.core.entities DEBUG 2024-09-12 12:56:57,332 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:56:57,333 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:56:57,339 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:56:57,356 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:56:57,383 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (68) Working directory for job is: /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs.runners DEBUG 2024-09-12 12:56:57,392 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [68] queued (53.728 ms) +galaxy.jobs.handler INFO 2024-09-12 12:56:57,398 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:56:57,401 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 68 +galaxy.jobs DEBUG 2024-09-12 12:56:57,493 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [68] prepared (71.754 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:57,494 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:56:57,494 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2: samtools:1.13 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:57,730 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.13--h8c37831_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:56:57,753 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/68/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/68/outputs/COMMAND_VERSION 2>&1; +samtools phase -b phase_wrapper -k 13 -q 37 -Q 13 -D 256 '/galaxy/server/database/objects/3/6/4/dataset_364f00e5-5045-4dcc-898d-0a5dd2b615fe.dat' > '/galaxy/server/database/objects/c/8/a/dataset_c8a289a6-9c88-4883-96fd-726dbdad45b4.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:56:57,795 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/68/working/phase_wrapper.0.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/68/working/phase_wrapper.0.bam" "/galaxy/server/database/objects/f/4/c/dataset_f4c80ccd-9e5d-4d94-bd2e-6549e8248dab.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/68/working/phase_wrapper.1.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/68/working/phase_wrapper.1.bam" "/galaxy/server/database/objects/9/f/c/dataset_9fc762c5-e9d4-4869-9449-65f962bc933b.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/68/working/phase_wrapper.chimera.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/68/working/phase_wrapper.chimera.bam" "/galaxy/server/database/objects/1/b/4/dataset_1b4f0186-fec6-498d-82e8-da6511f9d49e.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:57,808 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:56:57,808 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2: samtools:1.13 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:56:57,830 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.13--h8c37831_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:57:06,429 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:57:12,689 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2024-09-12 12:57:12,750 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.model.metadata DEBUG 2024-09-12 12:57:12,762 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.model.metadata DEBUG 2024-09-12 12:57:12,813 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.model.metadata DEBUG 2024-09-12 12:57:12,869 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.util WARNING 2024-09-12 12:57:12,921 [pN:job_handler_0,p:9,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/4/c/dataset_f4c80ccd-9e5d-4d94-bd2e-6549e8248dab.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/4/c/dataset_f4c80ccd-9e5d-4d94-bd2e-6549e8248dab.dat' +galaxy.util WARNING 2024-09-12 12:57:12,922 [pN:job_handler_0,p:9,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/9/f/c/dataset_9fc762c5-e9d4-4869-9449-65f962bc933b.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/f/c/dataset_9fc762c5-e9d4-4869-9449-65f962bc933b.dat' +galaxy.util WARNING 2024-09-12 12:57:12,922 [pN:job_handler_0,p:9,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/1/b/4/dataset_1b4f0186-fec6-498d-82e8-da6511f9d49e.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/b/4/dataset_1b4f0186-fec6-498d-82e8-da6511f9d49e.dat' +galaxy.jobs INFO 2024-09-12 12:57:12,956 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 68 in /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs DEBUG 2024-09-12 12:57:13,028 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 68 executed (309.904 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:57:16,044 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2024-09-12 12:57:16,083 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:57:16,084 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:57:16,090 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:57:16,107 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:57:16,127 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (69) Working directory for job is: /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs.runners DEBUG 2024-09-12 12:57:16,134 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [69] queued (44.732 ms) +galaxy.jobs.handler INFO 2024-09-12 12:57:16,139 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:57:16,145 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 69 +galaxy.jobs DEBUG 2024-09-12 12:57:16,264 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [69] prepared (96.941 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:57:16,287 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/69/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/69/registry.xml' '/galaxy/server/database/jobs_directory/000/69/upload_params.json' '85:/galaxy/server/database/objects/5/6/d/dataset_56db68ae-db4e-4bd3-bd86-220763a3ed04_files:/galaxy/server/database/objects/5/6/d/dataset_56db68ae-db4e-4bd3-bd86-220763a3ed04.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:57:16,302 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:57:26,724 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:57:32,843 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2024-09-12 12:57:32,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.jobs INFO 2024-09-12 12:57:32,997 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2024-09-12 12:57:33,055 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 69 executed (182.498 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:57:33,567 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2024-09-12 12:57:33,609 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:57:33,610 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:57:33,616 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:57:33,634 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:57:33,665 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (70) Working directory for job is: /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs.runners DEBUG 2024-09-12 12:57:33,674 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [70] queued (57.825 ms) +galaxy.jobs.handler INFO 2024-09-12 12:57:33,680 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:57:33,682 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 70 +galaxy.jobs DEBUG 2024-09-12 12:57:33,779 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [70] prepared (74.234 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:57:33,779 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:57:33,780 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2: samtools:1.13 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:57:33,806 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.13--h8c37831_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:57:33,830 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/70/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/70/outputs/COMMAND_VERSION 2>&1; +samtools phase -b phase_wrapper -k 13 -q 37 -Q 13 -D 256 -A '/galaxy/server/database/objects/5/6/d/dataset_56db68ae-db4e-4bd3-bd86-220763a3ed04.dat' > '/galaxy/server/database/objects/4/9/5/dataset_4952e1f5-b751-4a0e-b8c8-e11d7bedf2b4.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:57:33,875 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/70/working/phase_wrapper.0.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/70/working/phase_wrapper.0.bam" "/galaxy/server/database/objects/3/c/2/dataset_3c2d0b8f-483d-4bb4-9f94-d79d3a13feac.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/70/working/phase_wrapper.1.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/70/working/phase_wrapper.1.bam" "/galaxy/server/database/objects/f/2/5/dataset_f2506def-3b02-442b-93c1-1cf173b3ae1a.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/70/working/phase_wrapper.chimera.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/70/working/phase_wrapper.chimera.bam" "/galaxy/server/database/objects/f/0/e/dataset_f0ef3681-e195-455a-ab39-419a8e102a9f.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:57:33,887 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:57:33,887 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2: samtools:1.13 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:57:33,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.13--h8c37831_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:57:38,946 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 70: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:57:45,215 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 70 finished +galaxy.model.metadata DEBUG 2024-09-12 12:57:45,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.model.metadata DEBUG 2024-09-12 12:57:45,297 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.model.metadata DEBUG 2024-09-12 12:57:45,353 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 88 +galaxy.model.metadata DEBUG 2024-09-12 12:57:45,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 89 +galaxy.util WARNING 2024-09-12 12:57:45,476 [pN:job_handler_0,p:9,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/3/c/2/dataset_3c2d0b8f-483d-4bb4-9f94-d79d3a13feac.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/c/2/dataset_3c2d0b8f-483d-4bb4-9f94-d79d3a13feac.dat' +galaxy.util WARNING 2024-09-12 12:57:45,476 [pN:job_handler_0,p:9,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/2/5/dataset_f2506def-3b02-442b-93c1-1cf173b3ae1a.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/2/5/dataset_f2506def-3b02-442b-93c1-1cf173b3ae1a.dat' +galaxy.util WARNING 2024-09-12 12:57:45,477 [pN:job_handler_0,p:9,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/0/e/dataset_f0ef3681-e195-455a-ab39-419a8e102a9f.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/0/e/dataset_f0ef3681-e195-455a-ab39-419a8e102a9f.dat' +galaxy.jobs INFO 2024-09-12 12:57:45,511 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 70 in /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs DEBUG 2024-09-12 12:57:45,598 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 70 executed (352.491 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:57:48,034 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 71 +tpv.core.entities DEBUG 2024-09-12 12:57:48,077 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:57:48,077 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:57:48,084 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:57:48,103 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:57:48,126 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (71) Working directory for job is: /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs.runners DEBUG 2024-09-12 12:57:48,134 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [71] queued (50.412 ms) +galaxy.jobs.handler INFO 2024-09-12 12:57:48,139 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:57:48,145 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 71 +galaxy.jobs DEBUG 2024-09-12 12:57:48,263 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [71] prepared (95.940 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:57:48,287 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '90:/galaxy/server/database/objects/8/6/e/dataset_86eda187-6dd0-4c7f-b835-0d065af37d90_files:/galaxy/server/database/objects/8/6/e/dataset_86eda187-6dd0-4c7f-b835-0d065af37d90.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:57:48,303 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:57:59,192 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:58:05,378 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2024-09-12 12:58:05,474 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 90 +galaxy.jobs INFO 2024-09-12 12:58:05,577 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs DEBUG 2024-09-12 12:58:05,656 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 71 executed (245.785 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:58:06,723 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72 +tpv.core.entities DEBUG 2024-09-12 12:58:06,766 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:58:06,767 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:58:06,773 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:58:06,790 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:58:06,818 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (72) Working directory for job is: /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:06,829 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [72] queued (56.328 ms) +galaxy.jobs.handler INFO 2024-09-12 12:58:06,834 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:58:06,840 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 72 +galaxy.jobs DEBUG 2024-09-12 12:58:06,932 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [72] prepared (69.872 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:06,932 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:58:06,932 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2: samtools:1.13 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:06,959 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.13--h8c37831_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:58:06,984 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/72/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/72/outputs/COMMAND_VERSION 2>&1; +samtools phase -b phase_wrapper -F -k 13 -q 37 -Q 13 -D 256 '/galaxy/server/database/objects/8/6/e/dataset_86eda187-6dd0-4c7f-b835-0d065af37d90.dat' > '/galaxy/server/database/objects/a/5/4/dataset_a544ffe3-2ce1-4796-a10f-470ec12a4741.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:07,026 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/72/working/phase_wrapper.0.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/72/working/phase_wrapper.0.bam" "/galaxy/server/database/objects/4/9/1/dataset_49159a13-7799-4118-9da3-f2fa5933b499.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/72/working/phase_wrapper.1.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/72/working/phase_wrapper.1.bam" "/galaxy/server/database/objects/1/a/3/dataset_1a37dd76-5a71-4864-9999-58b3eaa7e25b.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/72/working/phase_wrapper.chimera.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/72/working/phase_wrapper.chimera.bam" "/galaxy/server/database/objects/2/4/d/dataset_24d95b40-5d69-4542-bdf3-47424304936f.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:07,039 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:58:07,039 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2: samtools:1.13 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:07,062 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.13--h8c37831_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:11,382 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 72: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:58:17,780 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 72 finished +galaxy.model.metadata DEBUG 2024-09-12 12:58:17,846 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.model.metadata DEBUG 2024-09-12 12:58:17,859 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.model.metadata DEBUG 2024-09-12 12:58:17,912 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.model.metadata DEBUG 2024-09-12 12:58:17,965 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.util WARNING 2024-09-12 12:58:18,019 [pN:job_handler_0,p:9,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/4/9/1/dataset_49159a13-7799-4118-9da3-f2fa5933b499.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_49159a13-7799-4118-9da3-f2fa5933b499.dat' +galaxy.util WARNING 2024-09-12 12:58:18,019 [pN:job_handler_0,p:9,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/a/3/dataset_1a37dd76-5a71-4864-9999-58b3eaa7e25b.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/a/3/dataset_1a37dd76-5a71-4864-9999-58b3eaa7e25b.dat' +galaxy.util WARNING 2024-09-12 12:58:18,020 [pN:job_handler_0,p:9,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/2/4/d/dataset_24d95b40-5d69-4542-bdf3-47424304936f.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/2/4/d/dataset_24d95b40-5d69-4542-bdf3-47424304936f.dat' +galaxy.jobs INFO 2024-09-12 12:58:18,053 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 72 in /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs DEBUG 2024-09-12 12:58:18,132 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 72 executed (321.207 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:58:22,220 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75, 73, 74 +tpv.core.entities DEBUG 2024-09-12 12:58:22,261 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:58:22,262 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:58:22,267 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:58:22,285 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:58:22,305 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (73) Working directory for job is: /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:22,313 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [73] queued (45.870 ms) +galaxy.jobs.handler INFO 2024-09-12 12:58:22,318 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:58:22,323 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 73 +tpv.core.entities DEBUG 2024-09-12 12:58:22,337 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:58:22,338 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:58:22,344 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:58:22,362 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:58:22,397 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (74) Working directory for job is: /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:22,408 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [74] queued (63.734 ms) +galaxy.jobs.handler INFO 2024-09-12 12:58:22,412 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:58:22,420 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 74 +tpv.core.entities DEBUG 2024-09-12 12:58:22,439 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:58:22,440 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:58:22,448 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:58:22,472 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:58:22,480 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [73] prepared (130.816 ms) +galaxy.jobs DEBUG 2024-09-12 12:58:22,516 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (75) Working directory for job is: /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs.command_factory INFO 2024-09-12 12:58:22,523 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/73/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/73/registry.xml' '/galaxy/server/database/jobs_directory/000/73/upload_params.json' '95:/galaxy/server/database/objects/3/f/f/dataset_3ffd00c3-a16c-443a-adb0-0c462972bd22_files:/galaxy/server/database/objects/3/f/f/dataset_3ffd00c3-a16c-443a-adb0-0c462972bd22.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:22,526 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [75] queued (78.162 ms) +galaxy.jobs.handler INFO 2024-09-12 12:58:22,532 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:58:22,538 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 75 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:22,549 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:58:22,592 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [74] prepared (135.426 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:58:22,628 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/74/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/74/registry.xml' '/galaxy/server/database/jobs_directory/000/74/upload_params.json' '96:/galaxy/server/database/objects/9/4/7/dataset_94765f7e-6527-490f-9af8-38f1c797ff57_files:/galaxy/server/database/objects/9/4/7/dataset_94765f7e-6527-490f-9af8-38f1c797ff57.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:22,642 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (74) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:58:22,689 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [75] prepared (119.234 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:58:22,713 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/75/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '97:/galaxy/server/database/objects/e/a/5/dataset_ea5ca88c-af9e-4403-8f69-1ab74165fce2_files:/galaxy/server/database/objects/e/a/5/dataset_ea5ca88c-af9e-4403-8f69-1ab74165fce2.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:22,728 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (75) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 12:58:23,535 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2024-09-12 12:58:23,578 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:58:23,578 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:58:23,585 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:58:23,605 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:58:23,628 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (76) Working directory for job is: /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:23,637 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [76] queued (51.348 ms) +galaxy.jobs.handler INFO 2024-09-12 12:58:23,642 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:58:23,647 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 76 +galaxy.jobs DEBUG 2024-09-12 12:58:23,769 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [76] prepared (97.439 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:58:23,792 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/76/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/76/registry.xml' '/galaxy/server/database/jobs_directory/000/76/upload_params.json' '98:/galaxy/server/database/objects/b/5/9/dataset_b5951084-af1f-4661-a78c-6e911d575ef4_files:/galaxy/server/database/objects/b/5/9/dataset_b5951084-af1f-4661-a78c-6e911d575ef4.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:23,810 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:58:33,291 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:58:33,312 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 12:58:33,333 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:58:33,363 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 12:58:46,690 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 73 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:58:46,777 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2024-09-12 12:58:46,863 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 95 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:46,900 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 75 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:58:46,902 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2024-09-12 12:58:46,907 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 96 +galaxy.jobs INFO 2024-09-12 12:58:47,035 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.model.metadata DEBUG 2024-09-12 12:58:47,040 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 98 +galaxy.model.metadata DEBUG 2024-09-12 12:58:47,048 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 97 +galaxy.jobs INFO 2024-09-12 12:58:47,078 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 74 in /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs INFO 2024-09-12 12:58:47,104 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2024-09-12 12:58:47,152 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 73 executed (381.537 ms) +galaxy.jobs INFO 2024-09-12 12:58:47,174 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 75 in /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs DEBUG 2024-09-12 12:58:47,187 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 74 executed (321.389 ms) +galaxy.jobs DEBUG 2024-09-12 12:58:47,200 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 76 executed (230.876 ms) +galaxy.jobs DEBUG 2024-09-12 12:58:47,240 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 75 executed (269.505 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:58:47,860 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 77 +tpv.core.entities DEBUG 2024-09-12 12:58:47,910 [pN:job_handler_0,p:9,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={'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/samtools_mpileup/samtools_mpileup/.*, abstract=False, cores=5, mem=cores * 3.8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:58:47,911 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:58:47,916 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:58:47,932 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:58:47,949 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (77) Working directory for job is: /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs.runners DEBUG 2024-09-12 12:58:47,960 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [77] queued (43.921 ms) +galaxy.jobs.handler INFO 2024-09-12 12:58:47,965 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:58:47,969 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 77 +galaxy.jobs DEBUG 2024-09-12 12:58:48,118 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [77] prepared (128.476 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:48,119 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:58:48,119 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:48,145 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:58:48,167 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/77/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/77/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/3/f/f/dataset_3ffd00c3-a16c-443a-adb0-0c462972bd22.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/a/8/6/metadata_a867a5f4-88a0-44d3-8694-24d6f645b165.dat' '0.bai' && ln -s '/galaxy/server/database/objects/9/4/7/dataset_94765f7e-6527-490f-9af8-38f1c797ff57.dat' '1' && ln -s '/galaxy/server/database/objects/_metadata_files/e/4/b/metadata_e4bea4ab-0e86-4916-812a-672a07c3d522.dat' '1.bai' && ln -s '/galaxy/server/database/objects/e/a/5/dataset_ea5ca88c-af9e-4403-8f69-1ab74165fce2.dat' '2' && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/3/metadata_803cd4df-3e21-4ce9-8c9f-30804ccb5fe5.dat' '2.bai' && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/b/5/9/dataset_b5951084-af1f-4661-a78c-6e911d575ef4.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools mpileup -f "$reffa" '0' '1' '2' -r '17:100-150' -C 0 -d 8000 -q 0 -Q 13 --output '/galaxy/server/database/objects/0/2/2/dataset_02282d75-4574-4383-a0db-cb6a1b2cb883.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:48,181 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (77) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:48,193 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:58:48,193 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:58:48,216 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:58:55,569 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 77: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 12:59:01,888 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 77 finished +galaxy.model.metadata DEBUG 2024-09-12 12:59:01,950 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.jobs INFO 2024-09-12 12:59:01,994 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 77 in /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs DEBUG 2024-09-12 12:59:02,053 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 77 executed (135.032 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:59:03,350 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79, 78 +tpv.core.entities DEBUG 2024-09-12 12:59:03,389 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:59:03,390 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:59:03,396 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:59:03,413 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:59:03,431 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (78) Working directory for job is: /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs.runners DEBUG 2024-09-12 12:59:03,439 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [78] queued (43.175 ms) +galaxy.jobs.handler INFO 2024-09-12 12:59:03,443 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:59:03,448 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 78 +tpv.core.entities DEBUG 2024-09-12 12:59:03,463 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:59:03,463 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:59:03,471 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:59:03,491 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:59:03,525 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (79) Working directory for job is: /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs.runners DEBUG 2024-09-12 12:59:03,534 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [79] queued (63.332 ms) +galaxy.jobs.handler INFO 2024-09-12 12:59:03,539 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:59:03,545 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 79 +galaxy.jobs DEBUG 2024-09-12 12:59:03,590 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [78] prepared (113.870 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:59:03,625 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '100:/galaxy/server/database/objects/d/d/1/dataset_dd16b33b-e82a-411d-8d42-ad5059595c61_files:/galaxy/server/database/objects/d/d/1/dataset_dd16b33b-e82a-411d-8d42-ad5059595c61.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:03,662 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:59:03,682 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [79] prepared (111.993 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:59:03,712 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/79/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/79/registry.xml' '/galaxy/server/database/jobs_directory/000/79/upload_params.json' '101:/galaxy/server/database/objects/b/a/c/dataset_bac673e3-0171-4b8f-901a-28b16e7e5cc3_files:/galaxy/server/database/objects/b/a/c/dataset_bac673e3-0171-4b8f-901a-28b16e7e5cc3.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:03,726 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (79) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:59:12,927 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:59:13,973 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 12:59:19,917 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2024-09-12 12:59:19,992 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.jobs INFO 2024-09-12 12:59:20,035 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs DEBUG 2024-09-12 12:59:20,092 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 79 executed (146.833 ms) +galaxy.jobs.runners DEBUG 2024-09-12 12:59:20,912 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 78 finished +galaxy.model.metadata DEBUG 2024-09-12 12:59:20,978 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs INFO 2024-09-12 12:59:21,110 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs DEBUG 2024-09-12 12:59:21,167 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 78 executed (225.270 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:59:22,017 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 80 +tpv.core.entities DEBUG 2024-09-12 12:59:22,065 [pN:job_handler_0,p:9,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={'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/samtools_mpileup/samtools_mpileup/.*, abstract=False, cores=5, mem=cores * 3.8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:59:22,066 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:59:22,072 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:59:22,089 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:59:22,110 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (80) Working directory for job is: /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs.runners DEBUG 2024-09-12 12:59:22,120 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [80] queued (48.542 ms) +galaxy.jobs.handler INFO 2024-09-12 12:59:22,125 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:59:22,130 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 80 +galaxy.jobs DEBUG 2024-09-12 12:59:22,236 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [80] prepared (84.816 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:22,237 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:59:22,237 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:22,264 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:59:22,288 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/80/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/d/d/1/dataset_dd16b33b-e82a-411d-8d42-ad5059595c61.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/f/7/1/metadata_f71cc2bc-393c-4c1c-bced-e7cb342c2b8e.dat' '0.bai' && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/b/a/c/dataset_bac673e3-0171-4b8f-901a-28b16e7e5cc3.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools mpileup -f "$reffa" '0' --rf 0 --ff 20 -r '17:1050-1060' -B -C 0 -d 8000 -q 0 -Q 13 --output '/galaxy/server/database/objects/1/d/6/dataset_1d694827-2b2e-482b-943e-876ab708428a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:22,304 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (80) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:22,316 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:59:22,317 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:22,340 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:28,148 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 80: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:59:34,326 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 80 finished +galaxy.model.metadata DEBUG 2024-09-12 12:59:34,393 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 102 +galaxy.jobs INFO 2024-09-12 12:59:34,439 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 80 in /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs DEBUG 2024-09-12 12:59:34,496 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 80 executed (137.903 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:59:36,494 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82, 81 +tpv.core.entities DEBUG 2024-09-12 12:59:36,536 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:59:36,536 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:59:36,544 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:59:36,561 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:59:36,581 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (81) Working directory for job is: /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs.runners DEBUG 2024-09-12 12:59:36,589 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [81] queued (44.280 ms) +galaxy.jobs.handler INFO 2024-09-12 12:59:36,593 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:59:36,599 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 81 +tpv.core.entities DEBUG 2024-09-12 12:59:36,612 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:59:36,612 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:59:36,619 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:59:36,637 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:59:36,673 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (82) Working directory for job is: /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs.runners DEBUG 2024-09-12 12:59:36,683 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [82] queued (63.920 ms) +galaxy.jobs.handler INFO 2024-09-12 12:59:36,688 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:59:36,696 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 82 +galaxy.jobs DEBUG 2024-09-12 12:59:36,739 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [81] prepared (115.353 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:59:36,774 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '103:/galaxy/server/database/objects/f/8/9/dataset_f89de5db-7942-4801-86c2-14af3bbd7a50_files:/galaxy/server/database/objects/f/8/9/dataset_f89de5db-7942-4801-86c2-14af3bbd7a50.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:36,790 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 12:59:36,837 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [82] prepared (116.168 ms) +galaxy.jobs.command_factory INFO 2024-09-12 12:59:36,862 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/82/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/82/registry.xml' '/galaxy/server/database/jobs_directory/000/82/upload_params.json' '104:/galaxy/server/database/objects/0/3/f/dataset_03f3aa72-fb1d-4942-acdf-017b46228f94_files:/galaxy/server/database/objects/0/3/f/dataset_03f3aa72-fb1d-4942-acdf-017b46228f94.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:36,877 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (82) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 12:59:46,590 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 81: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 12:59:46,609 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 2024-09-12 12:59:53,013 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 81 finished +galaxy.jobs.runners DEBUG 2024-09-12 12:59:53,087 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 82 finished +galaxy.model.metadata DEBUG 2024-09-12 12:59:53,093 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 103 +galaxy.model.metadata DEBUG 2024-09-12 12:59:53,166 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 104 +galaxy.jobs INFO 2024-09-12 12:59:53,193 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs INFO 2024-09-12 12:59:53,218 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs DEBUG 2024-09-12 12:59:53,255 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 81 executed (205.833 ms) +galaxy.jobs DEBUG 2024-09-12 12:59:53,277 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 82 executed (157.008 ms) +galaxy.jobs.handler DEBUG 2024-09-12 12:59:54,312 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2024-09-12 12:59:54,361 [pN:job_handler_0,p:9,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={'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/samtools_mpileup/samtools_mpileup/.*, abstract=False, cores=5, mem=cores * 3.8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 12:59:54,361 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 12:59:54,368 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 12:59:54,386 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 12:59:54,408 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (83) Working directory for job is: /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs.runners DEBUG 2024-09-12 12:59:54,419 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [83] queued (51.435 ms) +galaxy.jobs.handler INFO 2024-09-12 12:59:54,424 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 12:59:54,429 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 83 +galaxy.jobs DEBUG 2024-09-12 12:59:54,542 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [83] prepared (88.396 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:54,543 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:59:54,543 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:54,570 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 12:59:54,593 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/83/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/83/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/f/8/9/dataset_f89de5db-7942-4801-86c2-14af3bbd7a50.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/b/c/4/metadata_bc412258-b825-496d-9e7c-9b6e99658d99.dat' '0.bai' && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/0/3/f/dataset_03f3aa72-fb1d-4942-acdf-017b46228f94.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools mpileup -f "$reffa" '0' -O -s --output '/galaxy/server/database/objects/1/8/8/dataset_18856b0c-ebe2-47b4-ae03-868f0feb90d4.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:54,610 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (83) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:54,622 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 12:59:54,622 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 12:59:54,646 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 12:59:58,721 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:00:05,363 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2024-09-12 13:00:05,457 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 105 +galaxy.jobs INFO 2024-09-12 13:00:05,502 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2024-09-12 13:00:05,583 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 83 executed (188.673 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:00:07,789 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84, 85 +tpv.core.entities DEBUG 2024-09-12 13:00:07,830 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:07,830 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:07,837 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:00:07,856 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:00:07,876 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (84) Working directory for job is: /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs.runners DEBUG 2024-09-12 13:00:07,884 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [84] queued (47.341 ms) +galaxy.jobs.handler INFO 2024-09-12 13:00:07,888 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:07,894 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 84 +tpv.core.entities DEBUG 2024-09-12 13:00:07,907 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:07,907 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:07,914 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:00:07,931 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:00:07,967 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (85) Working directory for job is: /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs.runners DEBUG 2024-09-12 13:00:07,976 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [85] queued (61.932 ms) +galaxy.jobs.handler INFO 2024-09-12 13:00:07,980 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:07,987 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 85 +galaxy.jobs DEBUG 2024-09-12 13:00:08,035 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [84] prepared (116.532 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:00:08,069 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/84/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/84/registry.xml' '/galaxy/server/database/jobs_directory/000/84/upload_params.json' '106:/galaxy/server/database/objects/2/4/4/dataset_2447269b-bb94-444d-a89a-7e6ef27ffabf_files:/galaxy/server/database/objects/2/4/4/dataset_2447269b-bb94-444d-a89a-7e6ef27ffabf.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:00:08,088 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:00:08,138 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [85] prepared (125.610 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:00:08,164 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/85/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/85/registry.xml' '/galaxy/server/database/jobs_directory/000/85/upload_params.json' '107:/galaxy/server/database/objects/e/8/d/dataset_e8dfa894-f835-4854-96ab-f3a83b09494d_files:/galaxy/server/database/objects/e/8/d/dataset_e8dfa894-f835-4854-96ab-f3a83b09494d.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:00:08,180 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (85) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.runners.kubernetes ERROR 2024-09-12 13:00:17,071 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-qfk66 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-qfk66": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:17,126 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (85/gxy-qfk66) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-12 13:00:18,236 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 84: 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 2024-09-12 13:00:24,576 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 84 finished +galaxy.model.metadata DEBUG 2024-09-12 13:00:24,651 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 106 +galaxy.jobs INFO 2024-09-12 13:00:24,735 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 84 in /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs DEBUG 2024-09-12 13:00:24,797 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 84 executed (188.625 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:00:26,500 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 87, 86 +tpv.core.entities DEBUG 2024-09-12 13:00:26,540 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:26,541 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:26,547 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:00:26,566 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:00:26,587 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (86) Working directory for job is: /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs.runners DEBUG 2024-09-12 13:00:26,595 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [86] queued (47.729 ms) +galaxy.jobs.handler INFO 2024-09-12 13:00:26,602 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:26,604 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 86 +tpv.core.entities DEBUG 2024-09-12 13:00:26,620 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:26,621 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:26,628 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:00:26,646 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:00:26,680 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (87) Working directory for job is: /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs.runners DEBUG 2024-09-12 13:00:26,688 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [87] queued (60.181 ms) +galaxy.jobs.handler INFO 2024-09-12 13:00:26,692 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:26,699 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 87 +galaxy.jobs DEBUG 2024-09-12 13:00:26,745 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [86] prepared (112.699 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:00:26,781 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '108:/galaxy/server/database/objects/2/6/8/dataset_268c756d-344b-45cd-8afe-293500b8602d_files:/galaxy/server/database/objects/2/6/8/dataset_268c756d-344b-45cd-8afe-293500b8602d.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:00:26,819 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:00:26,838 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [87] prepared (109.226 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:00:26,869 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/87/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/87/registry.xml' '/galaxy/server/database/jobs_directory/000/87/upload_params.json' '109:/galaxy/server/database/objects/c/a/3/dataset_ca364a4f-ec8c-4355-bca3-afaba0e2dec8_files:/galaxy/server/database/objects/c/a/3/dataset_ca364a4f-ec8c-4355-bca3-afaba0e2dec8.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:00:26,884 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (87) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:00:37,043 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 87: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:00:38,067 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:00:43,673 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 87 finished +galaxy.model.metadata DEBUG 2024-09-12 13:00:43,742 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2024-09-12 13:00:43,785 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 87 in /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs DEBUG 2024-09-12 13:00:43,837 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 87 executed (133.037 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:00:44,586 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2024-09-12 13:00:44,654 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2024-09-12 13:00:44,735 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2024-09-12 13:00:44,788 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 86 executed (170.888 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:00:46,201 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 88 +tpv.core.entities DEBUG 2024-09-12 13:00:46,247 [pN:job_handler_0,p:9,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={'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/samtools_mpileup/samtools_mpileup/.*, abstract=False, cores=5, mem=cores * 3.8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:46,247 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:46,254 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:00:46,272 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:00:46,291 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (88) Working directory for job is: /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-09-12 13:00:46,303 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [88] queued (48.462 ms) +galaxy.jobs.handler INFO 2024-09-12 13:00:46,307 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:46,313 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 88 +galaxy.jobs DEBUG 2024-09-12 13:00:46,419 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [88] prepared (83.675 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:00:46,420 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:00:46,420 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:00:46,444 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:00:46,468 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/88/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/88/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/2/6/8/dataset_268c756d-344b-45cd-8afe-293500b8602d.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/d/8/a/metadata_d8acaf68-ce2e-4992-b7a4-f76035847178.dat' '0.bai' && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/c/a/3/dataset_ca364a4f-ec8c-4355-bca3-afaba0e2dec8.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools mpileup -f "$reffa" '0' -C 0 -d 8000 -q 0 -Q 0 -O -s --output '/galaxy/server/database/objects/5/6/b/dataset_56b3935c-39b8-49a6-a39b-4c00096b772a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:00:46,483 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (88) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:00:46,496 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:00:46,496 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:00:46,520 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:00:51,220 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 88: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:00:57,716 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2024-09-12 13:00:57,789 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 110 +galaxy.jobs INFO 2024-09-12 13:00:57,847 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 88 in /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs DEBUG 2024-09-12 13:00:57,904 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 88 executed (154.533 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:00:59,871 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90, 89 +tpv.core.entities DEBUG 2024-09-12 13:00:59,908 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:59,908 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:59,914 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:00:59,932 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:00:59,951 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (89) Working directory for job is: /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs.runners DEBUG 2024-09-12 13:00:59,959 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [89] queued (44.894 ms) +galaxy.jobs.handler INFO 2024-09-12 13:00:59,963 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:00:59,969 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 89 +tpv.core.entities DEBUG 2024-09-12 13:00:59,982 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:00:59,983 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:00:59,990 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:01:00,010 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:01:00,048 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (90) Working directory for job is: /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs.runners DEBUG 2024-09-12 13:01:00,058 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [90] queued (67.463 ms) +galaxy.jobs.handler INFO 2024-09-12 13:01:00,063 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:01:00,068 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 90 +galaxy.jobs DEBUG 2024-09-12 13:01:00,124 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [89] prepared (128.925 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:01:00,159 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '111:/galaxy/server/database/objects/2/7/b/dataset_27b8ec27-c12a-4047-aaac-b5b03d8ce280_files:/galaxy/server/database/objects/2/7/b/dataset_27b8ec27-c12a-4047-aaac-b5b03d8ce280.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:01:00,175 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:01:00,220 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [90] prepared (125.646 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:01:00,245 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/90/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/90/registry.xml' '/galaxy/server/database/jobs_directory/000/90/upload_params.json' '112:/galaxy/server/database/objects/5/f/1/dataset_5f18bd40-da47-44c8-aff6-423cf956b606_files:/galaxy/server/database/objects/5/f/1/dataset_5f18bd40-da47-44c8-aff6-423cf956b606.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:01:00,260 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (90) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:01:09,667 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 90: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:01:10,691 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 89: 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 2024-09-12 13:01:16,648 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 90 finished +galaxy.model.metadata DEBUG 2024-09-12 13:01:16,719 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 112 +galaxy.jobs INFO 2024-09-12 13:01:16,763 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 90 in /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs DEBUG 2024-09-12 13:01:16,820 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 90 executed (139.894 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:01:17,588 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 89 finished +galaxy.model.metadata DEBUG 2024-09-12 13:01:17,666 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 111 +galaxy.jobs INFO 2024-09-12 13:01:17,788 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 89 in /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs DEBUG 2024-09-12 13:01:17,844 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 89 executed (215.748 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:01:18,625 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 91 +tpv.core.entities DEBUG 2024-09-12 13:01:18,674 [pN:job_handler_0,p:9,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={'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/samtools_mpileup/samtools_mpileup/.*, abstract=False, cores=5, mem=cores * 3.8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:01:18,675 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:01:18,681 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:01:18,699 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:01:18,721 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (91) Working directory for job is: /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs.runners DEBUG 2024-09-12 13:01:18,732 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [91] queued (50.063 ms) +galaxy.jobs.handler INFO 2024-09-12 13:01:18,736 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:01:18,741 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 91 +galaxy.jobs DEBUG 2024-09-12 13:01:18,854 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [91] prepared (90.739 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:18,855 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:01:18,855 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:18,882 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:01:18,906 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/91/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/91/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/2/7/b/dataset_27b8ec27-c12a-4047-aaac-b5b03d8ce280.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/4/3/f/metadata_43f94c4e-91f1-4a4c-bb77-cb353a32707c.dat' '0.bai' && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/5/f/1/dataset_5f18bd40-da47-44c8-aff6-423cf956b606.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools mpileup -f "$reffa" '0' --output-extra 'NM,AM' --output '/galaxy/server/database/objects/1/1/1/dataset_111ea923-f357-4283-8652-b96b2adedf99.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:01:18,922 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (91) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:18,934 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:01:18,934 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7: samtools:1.15.1 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:18,957 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.15.1--h6899075_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:01:23,857 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:01:30,427 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2024-09-12 13:01:30,492 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 113 +galaxy.jobs INFO 2024-09-12 13:01:30,536 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 91 in /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs DEBUG 2024-09-12 13:01:30,584 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 91 executed (129.005 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:01:33,134 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 92 +tpv.core.entities DEBUG 2024-09-12 13:01:33,177 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:01:33,178 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:01:33,185 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:01:33,206 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:01:33,225 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (92) Working directory for job is: /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs.runners DEBUG 2024-09-12 13:01:33,234 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [92] queued (48.367 ms) +galaxy.jobs.handler INFO 2024-09-12 13:01:33,238 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:01:33,243 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 92 +galaxy.jobs DEBUG 2024-09-12 13:01:33,366 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [92] prepared (101.389 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:01:33,390 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/92/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/92/registry.xml' '/galaxy/server/database/jobs_directory/000/92/upload_params.json' '114:/galaxy/server/database/objects/c/0/3/dataset_c034a870-49be-45c0-8d6f-41bfb69ca909_files:/galaxy/server/database/objects/c/0/3/dataset_c034a870-49be-45c0-8d6f-41bfb69ca909.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:01:33,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:01:43,126 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 92: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:01:49,536 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 92 finished +galaxy.model.metadata DEBUG 2024-09-12 13:01:49,603 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 114 +galaxy.jobs INFO 2024-09-12 13:01:49,649 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs DEBUG 2024-09-12 13:01:49,698 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 92 executed (133.074 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:01:50,772 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 93 +tpv.core.entities DEBUG 2024-09-12 13:01:50,817 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:01:50,817 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:01:50,823 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:01:50,842 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:01:50,861 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (93) Working directory for job is: /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs.runners DEBUG 2024-09-12 13:01:50,870 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [93] queued (46.731 ms) +galaxy.jobs.handler INFO 2024-09-12 13:01:50,875 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:01:50,879 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 93 +galaxy.jobs DEBUG 2024-09-12 13:01:50,965 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [93] prepared (66.205 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:50,966 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:01:50,966 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 2024-09-12 13:01:51,162 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 2024-09-12 13:01:51,188 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/93/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/0/3/dataset_c034a870-49be-45c0-8d6f-41bfb69ca909.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools query --list-samples input.vcf.gz | tee /galaxy/server/database/objects/f/6/f/dataset_f6f7a9f1-cf41-4282-8ed4-ad82b68c6bfb.dat | tr '\n' ','] +galaxy.jobs.runners DEBUG 2024-09-12 13:01:51,206 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:51,219 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:01:51,219 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-12 13:01:51,238 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:01,348 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 93: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:02:07,679 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 93 finished +galaxy.model.metadata DEBUG 2024-09-12 13:02:07,752 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 115 +galaxy.jobs INFO 2024-09-12 13:02:07,794 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs DEBUG 2024-09-12 13:02:07,845 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 93 executed (133.753 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:02:10,374 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94, 95 +tpv.core.entities DEBUG 2024-09-12 13:02:10,415 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:02:10,416 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:02:10,421 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:02:10,437 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:02:10,457 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (94) Working directory for job is: /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs.runners DEBUG 2024-09-12 13:02:10,467 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [94] queued (45.524 ms) +galaxy.jobs.handler INFO 2024-09-12 13:02:10,471 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:02:10,477 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 94 +tpv.core.entities DEBUG 2024-09-12 13:02:10,491 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:02:10,492 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (95) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:02:10,499 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (95) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:02:10,517 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (95) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:02:10,551 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (95) Working directory for job is: /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs.runners DEBUG 2024-09-12 13:02:10,560 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [95] queued (60.781 ms) +galaxy.jobs.handler INFO 2024-09-12 13:02:10,564 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (95) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:02:10,569 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 95 +galaxy.jobs DEBUG 2024-09-12 13:02:10,620 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [94] prepared (115.998 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:02:10,652 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '116:/galaxy/server/database/objects/3/6/1/dataset_361253bb-25bf-4a64-95a1-a475f3db7433_files:/galaxy/server/database/objects/3/6/1/dataset_361253bb-25bf-4a64-95a1-a475f3db7433.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:10,668 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:02:10,710 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [95] prepared (117.504 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:02:10,736 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/95/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/95/registry.xml' '/galaxy/server/database/jobs_directory/000/95/upload_params.json' '117:/galaxy/server/database/objects/8/a/c/dataset_8acfbc0d-5b45-44a7-985b-2ad58066876e_files:/galaxy/server/database/objects/8/a/c/dataset_8acfbc0d-5b45-44a7-985b-2ad58066876e.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:10,751 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (95) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:02:20,271 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 95: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:02:21,298 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:02:27,005 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 95 finished +galaxy.model.metadata DEBUG 2024-09-12 13:02:27,073 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 117 +galaxy.jobs INFO 2024-09-12 13:02:27,119 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 95 in /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs DEBUG 2024-09-12 13:02:27,172 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 95 executed (136.154 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:02:28,005 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 94 finished +galaxy.model.metadata DEBUG 2024-09-12 13:02:28,072 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 116 +galaxy.jobs INFO 2024-09-12 13:02:28,109 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs DEBUG 2024-09-12 13:02:28,159 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 94 executed (121.077 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:02:29,050 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 96 +tpv.core.entities DEBUG 2024-09-12 13:02:29,096 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:02:29,097 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (96) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:02:29,103 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (96) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:02:29,120 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (96) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:02:29,139 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (96) Working directory for job is: /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs.runners DEBUG 2024-09-12 13:02:29,149 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [96] queued (45.639 ms) +galaxy.jobs.handler INFO 2024-09-12 13:02:29,155 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (96) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:02:29,158 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 96 +galaxy.jobs DEBUG 2024-09-12 13:02:29,282 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [96] prepared (103.181 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:02:29,283 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:02:29,283 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:02:29,307 [pN:job_handler_0,p:9,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 2024-09-12 13:02:29,333 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/96/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/96/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/6/1/dataset_361253bb-25bf-4a64-95a1-a475f3db7433.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/8/a/c/dataset_8acfbc0d-5b45-44a7-985b-2ad58066876e.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools isec --nfiles "=2" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/0/7/5/dataset_075f3793-0e1a-4beb-94ca-bb36a9981d6e.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:29,348 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (96) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:02:29,360 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:02:29,360 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-12 13:02:29,379 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:35,736 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 96: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:02:41,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 96 finished +galaxy.model.metadata DEBUG 2024-09-12 13:02:41,971 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 118 +galaxy.jobs INFO 2024-09-12 13:02:42,013 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 96 in /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs DEBUG 2024-09-12 13:02:42,063 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 96 executed (124.497 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:02:43,518 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 98, 97 +tpv.core.entities DEBUG 2024-09-12 13:02:43,557 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:02:43,558 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (97) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:02:43,565 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (97) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:02:43,582 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (97) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:02:43,602 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (97) Working directory for job is: /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs.runners DEBUG 2024-09-12 13:02:43,612 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [97] queued (46.221 ms) +galaxy.jobs.handler INFO 2024-09-12 13:02:43,616 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (97) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:02:43,622 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 97 +tpv.core.entities DEBUG 2024-09-12 13:02:43,636 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:02:43,637 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (98) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:02:43,644 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (98) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:02:43,663 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (98) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:02:43,696 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (98) Working directory for job is: /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs.runners DEBUG 2024-09-12 13:02:43,703 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [98] queued (59.141 ms) +galaxy.jobs.handler INFO 2024-09-12 13:02:43,707 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (98) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:02:43,713 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 98 +galaxy.jobs DEBUG 2024-09-12 13:02:43,760 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [97] prepared (111.682 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:02:43,791 [pN:job_handler_0,p:9,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' '119:/galaxy/server/database/objects/1/4/3/dataset_143ea450-55ff-4c22-956e-9d122de8fa19_files:/galaxy/server/database/objects/1/4/3/dataset_143ea450-55ff-4c22-956e-9d122de8fa19.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:43,805 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:02:43,839 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [98] prepared (103.806 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:02:43,863 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/98/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/98/registry.xml' '/galaxy/server/database/jobs_directory/000/98/upload_params.json' '120:/galaxy/server/database/objects/0/d/6/dataset_0d65ace0-2d11-4ff5-a0b9-d676dfad5c01_files:/galaxy/server/database/objects/0/d/6/dataset_0d65ace0-2d11-4ff5-a0b9-d676dfad5c01.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:02:43,876 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (98) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:02:53,176 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 97: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 13:02:53,194 [pN:job_handler_0,p:9,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 2024-09-12 13:03:00,013 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 97 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:03:00,053 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 98 finished +galaxy.model.metadata DEBUG 2024-09-12 13:03:00,088 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 119 +galaxy.model.metadata DEBUG 2024-09-12 13:03:00,130 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 120 +galaxy.jobs INFO 2024-09-12 13:03:00,141 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 97 in /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs INFO 2024-09-12 13:03:00,179 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 98 in /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs DEBUG 2024-09-12 13:03:00,214 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 97 executed (168.087 ms) +galaxy.jobs DEBUG 2024-09-12 13:03:00,239 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 98 executed (153.987 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:03:01,198 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 99 +tpv.core.entities DEBUG 2024-09-12 13:03:01,245 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:03:01,246 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (99) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:03:01,252 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (99) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:03:01,270 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (99) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:03:01,289 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (99) Working directory for job is: /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs.runners DEBUG 2024-09-12 13:03:01,300 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [99] queued (47.563 ms) +galaxy.jobs.handler INFO 2024-09-12 13:03:01,306 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (99) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:03:01,310 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 99 +galaxy.jobs DEBUG 2024-09-12 13:03:01,408 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [99] prepared (75.512 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:03:01,408 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:03:01,409 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:03:01,433 [pN:job_handler_0,p:9,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 2024-09-12 13:03:01,456 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/99/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/99/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/4/3/dataset_143ea450-55ff-4c22-956e-9d122de8fa19.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/0/d/6/dataset_0d65ace0-2d11-4ff5-a0b9-d676dfad5c01.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 ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/6/4/0/dataset_64086215-a423-4ef4-a4f6-1e3f581b1a51.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:01,471 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (99) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:03:01,484 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:03:01,484 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-12 13:03:01,504 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:06,340 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 99: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 13:03:12,614 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 99 finished +galaxy.model.metadata DEBUG 2024-09-12 13:03:12,683 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 121 +galaxy.jobs INFO 2024-09-12 13:03:12,728 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 99 in /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs DEBUG 2024-09-12 13:03:12,783 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 99 executed (138.841 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:03:15,672 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 101, 100 +tpv.core.entities DEBUG 2024-09-12 13:03:15,716 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:03:15,717 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (100) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:03:15,722 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (100) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:03:15,739 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (100) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:03:15,758 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (100) Working directory for job is: /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs.runners DEBUG 2024-09-12 13:03:15,766 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [100] queued (44.107 ms) +galaxy.jobs.handler INFO 2024-09-12 13:03:15,770 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (100) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:03:15,776 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 100 +tpv.core.entities DEBUG 2024-09-12 13:03:15,789 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:03:15,789 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (101) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:03:15,796 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (101) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:03:15,816 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (101) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:03:15,853 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (101) Working directory for job is: /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs.runners DEBUG 2024-09-12 13:03:15,862 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [101] queued (65.702 ms) +galaxy.jobs.handler INFO 2024-09-12 13:03:15,868 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (101) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:03:15,870 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 101 +galaxy.jobs DEBUG 2024-09-12 13:03:15,913 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [100] prepared (112.435 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:03:15,944 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '122:/galaxy/server/database/objects/e/2/f/dataset_e2f589c8-f231-492b-b994-306c5617db86_files:/galaxy/server/database/objects/e/2/f/dataset_e2f589c8-f231-492b-b994-306c5617db86.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:15,960 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:03:16,006 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [101] prepared (112.900 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:03:16,030 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/101/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/101/registry.xml' '/galaxy/server/database/jobs_directory/000/101/upload_params.json' '123:/galaxy/server/database/objects/e/3/8/dataset_e38410d9-276a-425d-81dc-e71d28a8a684_files:/galaxy/server/database/objects/e/3/8/dataset_e38410d9-276a-425d-81dc-e71d28a8a684.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:16,048 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (101) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 ERROR 2024-09-12 13:03:24,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (100/gxy-pxfkf) User killed running job, but error encountered during termination: Operation cannot be fulfilled on jobs.batch "gxy-pxfkf": the object has been modified; please apply your changes to the latest version and try again +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-pxfkf + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 908, in stop_job + self.__cleanup_k8s_job(k8s_job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-pxfkf": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-09-12 13:03:25,079 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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.handler DEBUG 2024-09-12 13:03:27,163 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 102 +tpv.core.entities DEBUG 2024-09-12 13:03:27,208 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:03:27,208 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (102) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:03:27,215 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (102) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:03:27,233 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (102) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:03:27,255 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (102) Working directory for job is: /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs.runners DEBUG 2024-09-12 13:03:27,264 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [102] queued (49.238 ms) +galaxy.jobs.handler INFO 2024-09-12 13:03:27,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (102) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:03:27,274 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 102 +galaxy.jobs DEBUG 2024-09-12 13:03:27,397 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [102] prepared (99.866 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:03:27,422 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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' '124:/galaxy/server/database/objects/f/5/5/dataset_f5575b0e-81c9-4010-8878-4750b6a7e550_files:/galaxy/server/database/objects/f/5/5/dataset_f5575b0e-81c9-4010-8878-4750b6a7e550.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:27,438 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:03:31,695 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 101 finished +galaxy.model.metadata DEBUG 2024-09-12 13:03:31,757 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 123 +galaxy.jobs INFO 2024-09-12 13:03:31,800 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 101 in /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs DEBUG 2024-09-12 13:03:31,852 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 101 executed (129.527 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:03:36,290 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 102: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 13:03:42,871 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 102 finished +galaxy.model.metadata DEBUG 2024-09-12 13:03:42,939 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 124 +galaxy.jobs INFO 2024-09-12 13:03:42,985 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 102 in /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs DEBUG 2024-09-12 13:03:43,047 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 102 executed (146.243 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:03:43,806 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 103 +tpv.core.entities DEBUG 2024-09-12 13:03:43,850 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:03:43,851 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (103) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:03:43,856 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (103) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:03:43,875 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (103) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:03:43,896 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (103) Working directory for job is: /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs.runners DEBUG 2024-09-12 13:03:43,905 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [103] queued (48.629 ms) +galaxy.jobs.handler INFO 2024-09-12 13:03:43,909 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (103) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:03:43,915 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 103 +galaxy.jobs DEBUG 2024-09-12 13:03:44,010 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [103] prepared (72.578 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:03:44,010 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:03:44,011 [pN:job_handler_0,p:9,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 2024-09-12 13:03:44,227 [pN:job_handler_0,p:9,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 2024-09-12 13:03:44,253 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/103/tool_script.sh] for tool command [vcfrandomsample -p 1 -r 0.2 '/galaxy/server/database/objects/f/5/5/dataset_f5575b0e-81c9-4010-8878-4750b6a7e550.dat' > '/galaxy/server/database/objects/c/a/4/dataset_ca4aa582-858c-4b0a-9cad-3caee84c6b89.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:44,270 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:03:44,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:03:44,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:03:44,305 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:03:55,821 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 103: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:04:02,319 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 103 finished +galaxy.model.metadata DEBUG 2024-09-12 13:04:02,387 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 125 +galaxy.jobs INFO 2024-09-12 13:04:02,444 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 103 in /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs DEBUG 2024-09-12 13:04:02,512 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 103 executed (162.084 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:04:05,500 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 104 +tpv.core.entities DEBUG 2024-09-12 13:04:05,559 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:04:05,560 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (104) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:04:05,566 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (104) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:04:05,587 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (104) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:04:05,609 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (104) Working directory for job is: /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs.runners DEBUG 2024-09-12 13:04:05,618 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [104] queued (51.969 ms) +galaxy.jobs.handler INFO 2024-09-12 13:04:05,623 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (104) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:04:05,629 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 104 +galaxy.jobs DEBUG 2024-09-12 13:04:05,804 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [104] prepared (126.310 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:04:05,829 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/104/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/104/registry.xml' '/galaxy/server/database/jobs_directory/000/104/upload_params.json' '126:/galaxy/server/database/objects/8/5/4/dataset_854eea0c-b07e-41b5-a964-6284ca75106b_files:/galaxy/server/database/objects/8/5/4/dataset_854eea0c-b07e-41b5-a964-6284ca75106b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:04:05,845 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:04:16,071 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 104: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:04:22,585 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 104 finished +galaxy.model.metadata DEBUG 2024-09-12 13:04:22,664 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 126 +galaxy.jobs INFO 2024-09-12 13:04:22,715 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 104 in /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs DEBUG 2024-09-12 13:04:22,778 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 104 executed (157.130 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:04:23,106 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 105 +tpv.core.entities DEBUG 2024-09-12 13:04:23,169 [pN:job_handler_0,p:9,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={'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/nanoplot/nanoplot/.*, abstract=False, cores=2, mem=12, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:04:23,170 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (105) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:04:23,181 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (105) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:04:23,212 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (105) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:04:23,247 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (105) Working directory for job is: /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs.runners DEBUG 2024-09-12 13:04:23,258 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [105] queued (77.047 ms) +galaxy.jobs.handler INFO 2024-09-12 13:04:23,262 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (105) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:04:23,269 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 105 +galaxy.jobs DEBUG 2024-09-12 13:04:23,398 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [105] prepared (102.895 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:04:23,398 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:04:23,399 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0: nanoplot:1.43.0 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:04:23,667 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:04:23,696 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/105/tool_script.sh] for tool command [NanoPlot --version > /galaxy/server/database/jobs_directory/000/105/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/8/5/4/dataset_854eea0c-b07e-41b5-a964-6284ca75106b.dat' './read_0.fastq.gz' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --fastq_rich read_0.fastq.gz --downsample 800 --plots kde -o '.' && >&2 cat *log] +galaxy.jobs.runners DEBUG 2024-09-12 13:04:23,740 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (105) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/105/working/NanoPlot-report.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/105/working/NanoPlot-report.html" "/galaxy/server/database/objects/5/8/a/dataset_58a742af-9543-4b59-a3cf-fe4f6b5a3bf5.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/105/working/NanoStats.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/105/working/NanoStats.txt" "/galaxy/server/database/objects/3/9/7/dataset_397d2452-4b5b-4391-bafa-b6f6cb208f7b.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/105/working/NanoStats_post_filtering.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/105/working/NanoStats_post_filtering.txt" "/galaxy/server/database/objects/8/d/b/dataset_8db2ad6e-8ac7-4cf7-a892-1e5051c7d802.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:04:23,757 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:04:23,757 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0: nanoplot:1.43.0 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:04:23,782 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:05:16,449 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 105: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:05:22,680 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 105 finished +galaxy.model.metadata DEBUG 2024-09-12 13:05:22,750 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 127 +galaxy.model.metadata DEBUG 2024-09-12 13:05:22,760 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 128 +galaxy.model.metadata DEBUG 2024-09-12 13:05:22,774 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 129 +galaxy.util WARNING 2024-09-12 13:05:22,785 [pN:job_handler_0,p:9,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/5/8/a/dataset_58a742af-9543-4b59-a3cf-fe4f6b5a3bf5.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/5/8/a/dataset_58a742af-9543-4b59-a3cf-fe4f6b5a3bf5.dat' +galaxy.util WARNING 2024-09-12 13:05:22,786 [pN:job_handler_0,p:9,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/3/9/7/dataset_397d2452-4b5b-4391-bafa-b6f6cb208f7b.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/3/9/7/dataset_397d2452-4b5b-4391-bafa-b6f6cb208f7b.dat' +galaxy.util WARNING 2024-09-12 13:05:22,786 [pN:job_handler_0,p:9,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/d/b/dataset_8db2ad6e-8ac7-4cf7-a892-1e5051c7d802.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/8/d/b/dataset_8db2ad6e-8ac7-4cf7-a892-1e5051c7d802.dat' +galaxy.jobs INFO 2024-09-12 13:05:22,831 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 105 in /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs DEBUG 2024-09-12 13:05:22,897 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 105 executed (185.058 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:05:26,075 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 106 +tpv.core.entities DEBUG 2024-09-12 13:05:26,115 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:05:26,116 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (106) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:05:26,121 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (106) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:05:26,140 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (106) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:05:26,160 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (106) Working directory for job is: /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs.runners DEBUG 2024-09-12 13:05:26,169 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [106] queued (47.041 ms) +galaxy.jobs.handler INFO 2024-09-12 13:05:26,173 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (106) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:05:26,178 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 106 +galaxy.jobs DEBUG 2024-09-12 13:05:26,301 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [106] prepared (100.852 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:05:26,326 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '130:/galaxy/server/database/objects/4/f/2/dataset_4f2bcdee-25c7-4455-a098-02bcc80b4316_files:/galaxy/server/database/objects/4/f/2/dataset_4f2bcdee-25c7-4455-a098-02bcc80b4316.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:05:26,342 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:05:36,868 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 106: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:05:43,200 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 106 finished +galaxy.model.metadata DEBUG 2024-09-12 13:05:43,268 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 130 +galaxy.jobs INFO 2024-09-12 13:05:43,349 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 106 in /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs DEBUG 2024-09-12 13:05:43,405 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 106 executed (173.843 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:05:44,652 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 107 +tpv.core.entities DEBUG 2024-09-12 13:05:44,698 [pN:job_handler_0,p:9,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={'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/nanoplot/nanoplot/.*, abstract=False, cores=2, mem=12, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:05:44,699 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (107) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:05:44,706 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (107) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:05:44,725 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (107) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:05:44,752 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (107) Working directory for job is: /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs.runners DEBUG 2024-09-12 13:05:44,761 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [107] queued (55.508 ms) +galaxy.jobs.handler INFO 2024-09-12 13:05:44,766 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (107) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:05:44,771 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 107 +galaxy.jobs DEBUG 2024-09-12 13:05:44,872 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [107] prepared (78.212 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:05:44,873 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:05:44,873 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0: nanoplot:1.43.0 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:05:44,897 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:05:44,920 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/107/tool_script.sh] for tool command [NanoPlot --version > /galaxy/server/database/jobs_directory/000/107/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/4/f/2/dataset_4f2bcdee-25c7-4455-a098-02bcc80b4316.dat' './read_0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/9/6/e/metadata_96e0e222-3d73-48c4-a8be-ccbf413ee512.dat' './read_0.bam.bai' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --bam read_0.bam --maxlength 2000 --color yellow -o '.' && >&2 cat *log] +galaxy.jobs.runners DEBUG 2024-09-12 13:05:44,953 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (107) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/107/working/NanoPlot-report.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/107/working/NanoPlot-report.html" "/galaxy/server/database/objects/0/8/5/dataset_085aa4ed-15a7-410d-9c83-f9271c33e33e.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/107/working/NanoStats.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/107/working/NanoStats.txt" "/galaxy/server/database/objects/a/4/5/dataset_a45d630e-9a59-4d78-b3f3-e8de2a8f9471.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/107/working/NanoStats_post_filtering.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/107/working/NanoStats_post_filtering.txt" "/galaxy/server/database/objects/3/1/0/dataset_310dac55-59af-4d1c-9d36-cb3c51ddb4e4.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:05:44,965 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:05:44,966 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0: nanoplot:1.43.0 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:05:44,988 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:05:59,302 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 107: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:06:05,882 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 107 finished +galaxy.model.metadata DEBUG 2024-09-12 13:06:05,954 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 131 +galaxy.model.metadata DEBUG 2024-09-12 13:06:05,964 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 132 +galaxy.model.metadata DEBUG 2024-09-12 13:06:06,001 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 133 +galaxy.util WARNING 2024-09-12 13:06:06,036 [pN:job_handler_0,p:9,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/0/8/5/dataset_085aa4ed-15a7-410d-9c83-f9271c33e33e.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/0/8/5/dataset_085aa4ed-15a7-410d-9c83-f9271c33e33e.dat' +galaxy.util WARNING 2024-09-12 13:06:06,037 [pN:job_handler_0,p:9,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/4/5/dataset_a45d630e-9a59-4d78-b3f3-e8de2a8f9471.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/4/5/dataset_a45d630e-9a59-4d78-b3f3-e8de2a8f9471.dat' +galaxy.jobs INFO 2024-09-12 13:06:06,080 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 107 in /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs DEBUG 2024-09-12 13:06:06,178 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 107 executed (261.098 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:06:07,374 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 108 +tpv.core.entities DEBUG 2024-09-12 13:06:07,420 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:06:07,421 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (108) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:06:07,427 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (108) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:06:07,447 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (108) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:06:07,469 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (108) Working directory for job is: /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs.runners DEBUG 2024-09-12 13:06:07,478 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [108] queued (50.318 ms) +galaxy.jobs.handler INFO 2024-09-12 13:06:07,484 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (108) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:07,489 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 108 +galaxy.jobs DEBUG 2024-09-12 13:06:07,635 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [108] prepared (120.400 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:06:07,666 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '134:/galaxy/server/database/objects/9/a/1/dataset_9a140251-4c09-4678-ab00-95f3d6a2785c_files:/galaxy/server/database/objects/9/a/1/dataset_9a140251-4c09-4678-ab00-95f3d6a2785c.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:06:07,683 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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.handler DEBUG 2024-09-12 13:06:08,487 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 109 +tpv.core.entities DEBUG 2024-09-12 13:06:08,529 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:06:08,530 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (109) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:06:08,535 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (109) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:06:08,555 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (109) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:06:08,574 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (109) Working directory for job is: /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs.runners DEBUG 2024-09-12 13:06:08,583 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [109] queued (47.301 ms) +galaxy.jobs.handler INFO 2024-09-12 13:06:08,589 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (109) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:08,592 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 109 +galaxy.jobs DEBUG 2024-09-12 13:06:08,712 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [109] prepared (98.174 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:06:08,735 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '135:/galaxy/server/database/objects/d/a/d/dataset_dad0eec8-6d14-484e-a2f4-b6b7adaff47a_files:/galaxy/server/database/objects/d/a/d/dataset_dad0eec8-6d14-484e-a2f4-b6b7adaff47a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:06:08,751 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:06:17,189 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 108: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:06:18,241 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 2024-09-12 13:06:23,728 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 108 finished +galaxy.model.metadata DEBUG 2024-09-12 13:06:23,803 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 134 +galaxy.jobs INFO 2024-09-12 13:06:23,848 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 108 in /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs DEBUG 2024-09-12 13:06:23,899 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 108 executed (139.165 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:06:24,758 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 109 finished +galaxy.model.metadata DEBUG 2024-09-12 13:06:24,824 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 135 +galaxy.jobs INFO 2024-09-12 13:06:24,863 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 109 in /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs DEBUG 2024-09-12 13:06:24,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 109 executed (119.138 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:06:25,172 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 110 +tpv.core.entities DEBUG 2024-09-12 13:06:25,221 [pN:job_handler_0,p:9,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={'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/nanoplot/nanoplot/.*, abstract=False, cores=2, mem=12, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:06:25,222 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (110) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:06:25,228 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (110) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:06:25,245 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (110) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:06:25,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (110) Working directory for job is: /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs.runners DEBUG 2024-09-12 13:06:25,280 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [110] queued (52.693 ms) +galaxy.jobs.handler INFO 2024-09-12 13:06:25,287 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (110) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:25,290 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 110 +galaxy.jobs DEBUG 2024-09-12 13:06:25,399 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [110] prepared (85.083 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:06:25,399 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:06:25,400 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0: nanoplot:1.43.0 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:06:25,425 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:06:25,468 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/110/tool_script.sh] for tool command [NanoPlot --version > /galaxy/server/database/jobs_directory/000/110/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/9/a/1/dataset_9a140251-4c09-4678-ab00-95f3d6a2785c.dat' './read_0.fasta' && ln -s '/galaxy/server/database/objects/d/a/d/dataset_dad0eec8-6d14-484e-a2f4-b6b7adaff47a.dat' './read_1.fasta' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --fasta read_0.fasta read_1.fasta -o '.' && >&2 cat *log] +galaxy.jobs.runners DEBUG 2024-09-12 13:06:25,509 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (110) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/110/working/NanoPlot-report.html" ] ; then cp "/galaxy/server/database/jobs_directory/000/110/working/NanoPlot-report.html" "/galaxy/server/database/objects/d/a/7/dataset_da732326-5805-42c6-a2cb-56bd79b0dd07.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/110/working/NanoStats.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/110/working/NanoStats.txt" "/galaxy/server/database/objects/c/b/9/dataset_cb9405ee-7eed-4979-b09c-0e37a1226c5a.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/110/working/NanoStats_post_filtering.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/110/working/NanoStats_post_filtering.txt" "/galaxy/server/database/objects/b/1/c/dataset_b1cb4b85-585a-4e27-88f5-85c3b5862441.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:06:25,523 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:06:25,523 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0: nanoplot:1.43.0 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:06:25,572 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-09-12 13:06:36,608 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-h46l9 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-h46l9": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:36,737 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (110/gxy-h46l9) Terminated at user's request +galaxy.util WARNING 2024-09-12 13:06:36,868 [pN:job_handler_0,p:9,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/d/a/7/dataset_da732326-5805-42c6-a2cb-56bd79b0dd07.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/a/7/dataset_da732326-5805-42c6-a2cb-56bd79b0dd07.dat' +galaxy.util WARNING 2024-09-12 13:06:36,869 [pN:job_handler_0,p:9,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/b/9/dataset_cb9405ee-7eed-4979-b09c-0e37a1226c5a.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/b/9/dataset_cb9405ee-7eed-4979-b09c-0e37a1226c5a.dat' +galaxy.jobs.handler DEBUG 2024-09-12 13:06:39,658 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 111 +tpv.core.entities DEBUG 2024-09-12 13:06:39,700 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:06:39,701 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (111) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:06:39,707 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (111) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:06:39,726 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (111) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:06:39,744 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (111) Working directory for job is: /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs.runners DEBUG 2024-09-12 13:06:39,753 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [111] queued (45.230 ms) +galaxy.jobs.handler INFO 2024-09-12 13:06:39,757 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (111) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:39,764 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 111 +galaxy.jobs DEBUG 2024-09-12 13:06:39,885 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [111] prepared (99.082 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:06:39,908 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '139:/galaxy/server/database/objects/7/9/8/dataset_7981659c-c0f5-4386-99aa-40c089d3fdc5_files:/galaxy/server/database/objects/7/9/8/dataset_7981659c-c0f5-4386-99aa-40c089d3fdc5.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:06:39,922 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 ERROR 2024-09-12 13:06:48,971 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-95rb2 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-95rb2": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:49,017 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (111/gxy-95rb2) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-12 13:06:51,030 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 112 +tpv.core.entities DEBUG 2024-09-12 13:06:51,072 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:06:51,072 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (112) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:06:51,078 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (112) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:06:51,096 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (112) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:06:51,116 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (112) Working directory for job is: /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs.runners DEBUG 2024-09-12 13:06:51,125 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [112] queued (46.697 ms) +galaxy.jobs.handler INFO 2024-09-12 13:06:51,130 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (112) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:06:51,134 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 112 +galaxy.jobs DEBUG 2024-09-12 13:06:51,257 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [112] prepared (99.265 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:06:51,279 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '140:/galaxy/server/database/objects/0/2/0/dataset_02080b6e-0f9b-470d-b5d3-4fe0c1d76606_files:/galaxy/server/database/objects/0/2/0/dataset_02080b6e-0f9b-470d-b5d3-4fe0c1d76606.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:06:51,298 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:07:01,393 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 112: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:07:08,179 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 112 finished +galaxy.model.metadata DEBUG 2024-09-12 13:07:08,250 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 140 +galaxy.jobs INFO 2024-09-12 13:07:08,291 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 112 in /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs DEBUG 2024-09-12 13:07:08,340 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 112 executed (128.765 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:07:09,667 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 113 +tpv.core.entities DEBUG 2024-09-12 13:07:09,717 [pN:job_handler_0,p:9,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={'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_extract/poretools_extract/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:07:09,717 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (113) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:07:09,726 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (113) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:07:09,745 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (113) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:07:09,764 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (113) Working directory for job is: /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs.runners DEBUG 2024-09-12 13:07:09,775 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [113] queued (48.312 ms) +galaxy.jobs.handler INFO 2024-09-12 13:07:09,779 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (113) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:07:09,785 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 113 +galaxy.jobs DEBUG 2024-09-12 13:07:09,884 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [113] prepared (75.370 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:07:09,884 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:07:09,885 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:07:10,088 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:07:10,112 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/113/tool_script.sh] for tool command [poretools fasta --type all --min-length 0 --max-length 1000000000 '/galaxy/server/database/objects/0/2/0/dataset_02080b6e-0f9b-470d-b5d3-4fe0c1d76606.dat' > '/galaxy/server/database/objects/c/c/2/dataset_cc2791c3-e807-425c-aa87-9bee2c1293eb.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:07:10,128 [pN:job_handler_0,p:9,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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:07:10,142 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:07:10,143 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:07:10,164 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:07:39,164 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 113: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:07:45,255 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 113 finished +galaxy.model.metadata DEBUG 2024-09-12 13:07:45,319 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 141 +galaxy.jobs INFO 2024-09-12 13:07:45,364 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 113 in /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs DEBUG 2024-09-12 13:07:45,411 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 113 executed (125.509 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:07:47,763 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 114 +tpv.core.entities DEBUG 2024-09-12 13:07:47,799 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:07:47,799 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (114) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:07:47,804 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (114) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:07:47,821 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (114) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:07:47,838 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (114) Working directory for job is: /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs.runners DEBUG 2024-09-12 13:07:47,845 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [114] queued (40.797 ms) +galaxy.jobs.handler INFO 2024-09-12 13:07:47,849 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (114) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:07:47,854 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 114 +galaxy.jobs DEBUG 2024-09-12 13:07:47,957 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [114] prepared (84.173 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:07:47,978 [pN:job_handler_0,p:9,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' '142:/galaxy/server/database/objects/d/0/b/dataset_d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea_files:/galaxy/server/database/objects/d/0/b/dataset_d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:07:47,991 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:07:58,439 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 114: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:08:04,688 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 114 finished +galaxy.model.metadata DEBUG 2024-09-12 13:08:04,754 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 142 +galaxy.jobs INFO 2024-09-12 13:08:04,840 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 114 in /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs DEBUG 2024-09-12 13:08:04,899 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 114 executed (181.364 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:08:06,308 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 115 +tpv.core.entities DEBUG 2024-09-12 13:08:06,354 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:08:06,354 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (115) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:08:06,361 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (115) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:08:06,379 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (115) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:08:06,401 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (115) Working directory for job is: /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs.runners DEBUG 2024-09-12 13:08:06,411 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [115] queued (49.961 ms) +galaxy.jobs.handler INFO 2024-09-12 13:08:06,416 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (115) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:08:06,421 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 115 +galaxy.jobs DEBUG 2024-09-12 13:08:06,542 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [115] prepared (99.650 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:08:06,543 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:08:06,543 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 2024-09-12 13:08:06,741 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 2024-09-12 13:08:06,765 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/115/tool_script.sh] for tool command [plotFingerprint --version > /galaxy/server/database/jobs_directory/000/115/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/d/0/b/dataset_d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/1/metadata_8014a213-3e17-4886-a8bc-1311216ae213.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/d/0/b/dataset_d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/1/metadata_8014a213-3e17-4886-a8bc-1311216ae213.dat' './1.bam.bai' && plotFingerprint --numberOfProcessors "${GALAXY_SLOTS:-4}" --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFile /galaxy/server/database/objects/e/7/8/dataset_e7828476-49b3-49f3-9f48-e3757769d5f5.dat --plotFileFormat 'png'] +galaxy.jobs.runners DEBUG 2024-09-12 13:08:06,781 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (115) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:08:06,794 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:08:06,794 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:08:06,815 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:08:37,157 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 115: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:08:43,235 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 115 finished +galaxy.model.metadata DEBUG 2024-09-12 13:08:43,297 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 143 +galaxy.util WARNING 2024-09-12 13:08:43,303 [pN:job_handler_0,p:9,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/e/7/8/dataset_e7828476-49b3-49f3-9f48-e3757769d5f5.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/7/8/dataset_e7828476-49b3-49f3-9f48-e3757769d5f5.dat' +galaxy.jobs INFO 2024-09-12 13:08:43,335 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 115 in /galaxy/server/database/jobs_directory/000/115 +galaxy.objectstore CRITICAL 2024-09-12 13:08:43,377 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs DEBUG 2024-09-12 13:08:43,377 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 115 executed (113.881 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:08:45,448 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 117, 116 +tpv.core.entities DEBUG 2024-09-12 13:08:45,500 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:08:45,501 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (116) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:08:45,508 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (116) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:08:45,525 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (116) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:08:45,569 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (116) Working directory for job is: /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs.runners DEBUG 2024-09-12 13:08:45,577 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [116] queued (68.831 ms) +galaxy.jobs.handler INFO 2024-09-12 13:08:45,581 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (116) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:08:45,586 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 116 +tpv.core.entities DEBUG 2024-09-12 13:08:45,601 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:08:45,602 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (117) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:08:45,611 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (117) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:08:45,660 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (117) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:08:45,698 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (117) Working directory for job is: /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs.runners DEBUG 2024-09-12 13:08:45,706 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [117] queued (95.605 ms) +galaxy.jobs.handler INFO 2024-09-12 13:08:45,713 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (117) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:08:45,717 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 117 +galaxy.jobs DEBUG 2024-09-12 13:08:45,793 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [116] prepared (179.700 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:08:45,822 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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' '144:/galaxy/server/database/objects/e/0/1/dataset_e0123935-c035-4e21-a490-bf2a545c1877_files:/galaxy/server/database/objects/e/0/1/dataset_e0123935-c035-4e21-a490-bf2a545c1877.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:08:45,852 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:08:45,876 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [117] prepared (99.498 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:08:45,899 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/117/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/117/registry.xml' '/galaxy/server/database/jobs_directory/000/117/upload_params.json' '145:/galaxy/server/database/objects/3/e/3/dataset_3e32ed29-1dc8-4673-a182-bafe2b392107_files:/galaxy/server/database/objects/3/e/3/dataset_3e32ed29-1dc8-4673-a182-bafe2b392107.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:08:45,912 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (117) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:08:55,983 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 117: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:08:56,996 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 116: 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 2024-09-12 13:09:02,461 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 117 finished +galaxy.model.metadata DEBUG 2024-09-12 13:09:02,531 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 145 +galaxy.jobs INFO 2024-09-12 13:09:02,619 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 117 in /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs DEBUG 2024-09-12 13:09:02,675 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 117 executed (182.324 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:09:03,472 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 116 finished +galaxy.model.metadata DEBUG 2024-09-12 13:09:03,538 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 144 +galaxy.jobs INFO 2024-09-12 13:09:03,622 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 116 in /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs DEBUG 2024-09-12 13:09:03,680 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 116 executed (176.589 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:09:04,224 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 118 +tpv.core.entities DEBUG 2024-09-12 13:09:04,266 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:09:04,267 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (118) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:09:04,273 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (118) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:09:04,291 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (118) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:09:04,316 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (118) Working directory for job is: /galaxy/server/database/jobs_directory/000/118 +galaxy.jobs.runners DEBUG 2024-09-12 13:09:04,327 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [118] queued (54.632 ms) +galaxy.jobs.handler INFO 2024-09-12 13:09:04,332 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (118) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:09:04,338 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 118 +galaxy.jobs DEBUG 2024-09-12 13:09:04,442 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [118] prepared (82.419 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:09:04,443 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:09:04,443 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 2024-09-12 13:09:04,469 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 2024-09-12 13:09:04,494 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/118/tool_script.sh] for tool command [plotFingerprint --version > /galaxy/server/database/jobs_directory/000/118/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/3/e/3/dataset_3e32ed29-1dc8-4673-a182-bafe2b392107.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/3/2/5/metadata_3250c116-496e-4577-8a75-c473e8459824.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/3/e/3/dataset_3e32ed29-1dc8-4673-a182-bafe2b392107.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/3/2/5/metadata_3250c116-496e-4577-8a75-c473e8459824.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/5/1/8/dataset_51817478-8918-4804-9ab3-3083e76b6d49.dat --plotFileFormat png --outRawCounts '/galaxy/server/database/objects/e/2/2/dataset_e228c695-27f7-4b5b-aec9-d1a91098c61a.dat' --outQualityMetrics '/galaxy/server/database/objects/f/3/4/dataset_f34cd567-9074-4d84-abf5-4758373d9b9c.dat' --JSDsample '0.bam' --binSize '500' --numberOfSamples '100000' --plotTitle 'Test Fingerprint Plot' --minMappingQuality '1'] +galaxy.jobs.runners DEBUG 2024-09-12 13:09:04,524 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:09:04,537 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:09:04,537 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:09:04,558 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:09:36,865 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 118: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:09:43,042 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 118 finished +galaxy.model.metadata DEBUG 2024-09-12 13:09:43,104 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 146 +galaxy.model.metadata DEBUG 2024-09-12 13:09:43,113 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 147 +galaxy.model.metadata DEBUG 2024-09-12 13:09:43,125 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 148 +galaxy.util WARNING 2024-09-12 13:09:43,134 [pN:job_handler_0,p:9,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/5/1/8/dataset_51817478-8918-4804-9ab3-3083e76b6d49.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/5/1/8/dataset_51817478-8918-4804-9ab3-3083e76b6d49.dat' +galaxy.util WARNING 2024-09-12 13:09:43,135 [pN:job_handler_0,p:9,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/2/2/dataset_e228c695-27f7-4b5b-aec9-d1a91098c61a.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/2/2/dataset_e228c695-27f7-4b5b-aec9-d1a91098c61a.dat' +galaxy.util WARNING 2024-09-12 13:09:43,136 [pN:job_handler_0,p:9,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/f/3/4/dataset_f34cd567-9074-4d84-abf5-4758373d9b9c.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/3/4/dataset_f34cd567-9074-4d84-abf5-4758373d9b9c.dat' +galaxy.jobs INFO 2024-09-12 13:09:43,172 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 118 in /galaxy/server/database/jobs_directory/000/118 +galaxy.objectstore CRITICAL 2024-09-12 13:09:43,220 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs DEBUG 2024-09-12 13:09:43,221 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 118 executed (149.916 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:09:46,476 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 119 +tpv.core.entities DEBUG 2024-09-12 13:09:46,519 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:09:46,519 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (119) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:09:46,526 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (119) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:09:46,543 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (119) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:09:46,561 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (119) Working directory for job is: /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs.runners DEBUG 2024-09-12 13:09:46,570 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [119] queued (44.043 ms) +galaxy.jobs.handler INFO 2024-09-12 13:09:46,574 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (119) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:09:46,579 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 119 +galaxy.jobs DEBUG 2024-09-12 13:09:46,701 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [119] prepared (100.172 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:09:46,723 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '149:/galaxy/server/database/objects/5/9/3/dataset_5933cea0-c94c-4c28-86aa-cea36ef33791_files:/galaxy/server/database/objects/5/9/3/dataset_5933cea0-c94c-4c28-86aa-cea36ef33791.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:09:46,737 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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.handler DEBUG 2024-09-12 13:09:47,577 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 120 +tpv.core.entities DEBUG 2024-09-12 13:09:47,616 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:09:47,617 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (120) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:09:47,622 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (120) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:09:47,639 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (120) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:09:47,657 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (120) Working directory for job is: /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs.runners DEBUG 2024-09-12 13:09:47,665 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [120] queued (42.613 ms) +galaxy.jobs.handler INFO 2024-09-12 13:09:47,670 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (120) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:09:47,675 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 120 +galaxy.jobs DEBUG 2024-09-12 13:09:47,794 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [120] prepared (95.370 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:09:47,814 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/120/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/120/registry.xml' '/galaxy/server/database/jobs_directory/000/120/upload_params.json' '150:/galaxy/server/database/objects/7/7/b/dataset_77b907a7-574a-49e6-977b-68cba0624d9f_files:/galaxy/server/database/objects/7/7/b/dataset_77b907a7-574a-49e6-977b-68cba0624d9f.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:09:47,829 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:09:57,287 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 119: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:09:57,313 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] 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 2024-09-12 13:10:03,957 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 119 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:10:03,965 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 120 finished +galaxy.model.metadata DEBUG 2024-09-12 13:10:04,046 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 149 +galaxy.model.metadata DEBUG 2024-09-12 13:10:04,047 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 150 +galaxy.jobs INFO 2024-09-12 13:10:04,106 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 120 in /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs INFO 2024-09-12 13:10:04,167 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 119 in /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs DEBUG 2024-09-12 13:10:04,201 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 120 executed (201.267 ms) +galaxy.jobs DEBUG 2024-09-12 13:10:04,238 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 119 executed (241.769 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:10:05,165 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 121 +tpv.core.entities DEBUG 2024-09-12 13:10:05,215 [pN:job_handler_0,p:9,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={'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_call/lofreq_call/.*, abstract=False, cores=2, mem=8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:05,215 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (121) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:05,222 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (121) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:05,240 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (121) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:05,259 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (121) Working directory for job is: /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:05,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [121] queued (47.635 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:05,274 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (121) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:05,279 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 121 +galaxy.jobs DEBUG 2024-09-12 13:10:05,462 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [121] prepared (160.896 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:05,463 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:10:05,463 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:05,723 [pN:job_handler_0,p:9,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 2024-09-12 13:10:05,749 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/121/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/121/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/7/7/b/dataset_77b907a7-574a-49e6-977b-68cba0624d9f.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/galaxy/server/database/objects/5/9/3/dataset_5933cea0-c94c-4c28-86aa-cea36ef33791.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/b/f/7/metadata_bf747e1a-a9de-4833-8eb1-c036ece3d644.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:05,768 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (121) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/121/working/variants.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/121/working/variants.vcf" "/galaxy/server/database/objects/c/e/3/dataset_ce3cfd93-1566-4706-a6a0-8774b6085e23.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:05,781 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:10:05,782 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:05,805 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:17,583 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 121: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:10:23,689 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 121 finished +galaxy.model.metadata DEBUG 2024-09-12 13:10:23,759 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 151 +galaxy.util WARNING 2024-09-12 13:10:23,769 [pN:job_handler_0,p:9,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/c/e/3/dataset_ce3cfd93-1566-4706-a6a0-8774b6085e23.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/e/3/dataset_ce3cfd93-1566-4706-a6a0-8774b6085e23.dat' +galaxy.jobs INFO 2024-09-12 13:10:23,814 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 121 in /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs DEBUG 2024-09-12 13:10:23,867 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 121 executed (145.285 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:10:25,831 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 122, 123 +tpv.core.entities DEBUG 2024-09-12 13:10:25,871 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:25,872 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (122) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:25,878 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (122) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:25,896 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (122) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:25,913 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (122) Working directory for job is: /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:25,922 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [122] queued (43.793 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:25,926 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (122) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:25,931 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 122 +tpv.core.entities DEBUG 2024-09-12 13:10:25,942 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:25,942 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (123) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:25,949 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (123) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:25,969 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (123) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:26,008 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (123) Working directory for job is: /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:26,017 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [123] queued (67.575 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:26,022 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (123) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:26,028 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 123 +galaxy.jobs DEBUG 2024-09-12 13:10:26,079 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [122] prepared (121.447 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:10:26,114 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/122/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/122/registry.xml' '/galaxy/server/database/jobs_directory/000/122/upload_params.json' '152:/galaxy/server/database/objects/8/5/c/dataset_85c05234-1333-4459-bdb1-047d5dde965f_files:/galaxy/server/database/objects/8/5/c/dataset_85c05234-1333-4459-bdb1-047d5dde965f.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:26,132 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:10:26,170 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [123] prepared (113.914 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:10:26,194 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/123/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/123/registry.xml' '/galaxy/server/database/jobs_directory/000/123/upload_params.json' '153:/galaxy/server/database/objects/d/4/d/dataset_d4dfb13b-9d55-416e-8767-f0b93119a420_files:/galaxy/server/database/objects/d/4/d/dataset_d4dfb13b-9d55-416e-8767-f0b93119a420.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:26,209 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (123) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:10:36,092 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 122: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:10:36,117 [pN:job_handler_0,p:9,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 2024-09-12 13:10:42,501 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 122 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:10:42,550 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 123 finished +galaxy.model.metadata DEBUG 2024-09-12 13:10:42,579 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 152 +galaxy.model.metadata DEBUG 2024-09-12 13:10:42,629 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 153 +galaxy.jobs INFO 2024-09-12 13:10:42,686 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 122 in /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs INFO 2024-09-12 13:10:42,693 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 123 in /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs DEBUG 2024-09-12 13:10:42,744 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 122 executed (211.291 ms) +galaxy.jobs DEBUG 2024-09-12 13:10:42,748 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 123 executed (163.327 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:10:43,602 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 124 +tpv.core.entities DEBUG 2024-09-12 13:10:43,651 [pN:job_handler_0,p:9,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={'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_call/lofreq_call/.*, abstract=False, cores=2, mem=8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:43,652 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (124) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:43,658 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (124) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:43,678 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (124) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:43,698 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (124) Working directory for job is: /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:43,708 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [124] queued (49.689 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:43,713 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (124) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:43,718 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 124 +galaxy.jobs DEBUG 2024-09-12 13:10:43,820 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [124] prepared (81.180 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:43,821 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:10:43,821 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:43,848 [pN:job_handler_0,p:9,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 2024-09-12 13:10:43,872 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/124/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/124/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/d/4/d/dataset_d4dfb13b-9d55-416e-8767-f0b93119a420.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/galaxy/server/database/objects/8/5/c/dataset_85c05234-1333-4459-bdb1-047d5dde965f.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/2/7/5/metadata_27594236-acce-4826-a976-aec022248217.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:43,889 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (124) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/124/working/variants.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/124/working/variants.vcf" "/galaxy/server/database/objects/9/5/f/dataset_95fb20f0-16db-4722-a169-c2e195de5ff3.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:43,901 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:10:43,901 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:10:43,927 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:50,277 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 124: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:10:56,585 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 124 finished +galaxy.model.metadata DEBUG 2024-09-12 13:10:56,656 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 154 +galaxy.util WARNING 2024-09-12 13:10:56,666 [pN:job_handler_0,p:9,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/9/5/f/dataset_95fb20f0-16db-4722-a169-c2e195de5ff3.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_95fb20f0-16db-4722-a169-c2e195de5ff3.dat' +galaxy.jobs INFO 2024-09-12 13:10:56,701 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 124 in /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs DEBUG 2024-09-12 13:10:56,756 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 124 executed (137.068 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:10:58,087 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 126, 125 +tpv.core.entities DEBUG 2024-09-12 13:10:58,129 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:58,129 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (125) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:58,136 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (125) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:58,154 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (125) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:58,175 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (125) Working directory for job is: /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:58,182 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [125] queued (46.149 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:58,187 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (125) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:58,193 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 125 +tpv.core.entities DEBUG 2024-09-12 13:10:58,206 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:58,207 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (126) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:58,214 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (126) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:58,242 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (126) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:58,274 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (126) Working directory for job is: /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:58,284 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [126] queued (70.333 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:58,290 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (126) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:58,295 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 126 +galaxy.jobs DEBUG 2024-09-12 13:10:58,324 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [125] prepared (108.740 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:10:58,350 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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' '155:/galaxy/server/database/objects/c/4/e/dataset_c4ef6f65-10b5-450e-9b43-ef723818cf0b_files:/galaxy/server/database/objects/c/4/e/dataset_c4ef6f65-10b5-450e-9b43-ef723818cf0b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:58,374 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:10:58,436 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [126] prepared (114.053 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:10:58,459 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/126/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/126/registry.xml' '/galaxy/server/database/jobs_directory/000/126/upload_params.json' '156:/galaxy/server/database/objects/a/1/6/dataset_a160720b-e062-4f72-9197-c5b80f55b0ba_files:/galaxy/server/database/objects/a/1/6/dataset_a160720b-e062-4f72-9197-c5b80f55b0ba.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:58,475 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (126) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 13:10:59,293 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 127 +tpv.core.entities DEBUG 2024-09-12 13:10:59,337 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:10:59,338 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (127) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:10:59,344 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (127) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:10:59,364 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (127) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:10:59,384 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (127) Working directory for job is: /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs.runners DEBUG 2024-09-12 13:10:59,392 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [127] queued (47.628 ms) +galaxy.jobs.handler INFO 2024-09-12 13:10:59,397 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (127) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:10:59,402 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 127 +galaxy.jobs DEBUG 2024-09-12 13:10:59,533 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [127] prepared (107.917 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:10:59,559 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/127/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/127/registry.xml' '/galaxy/server/database/jobs_directory/000/127/upload_params.json' '157:/galaxy/server/database/objects/1/a/6/dataset_1a6993a6-b3a3-4df0-a8dc-4484467b2b35_files:/galaxy/server/database/objects/1/a/6/dataset_1a6993a6-b3a3-4df0-a8dc-4484467b2b35.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:10:59,574 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:11:08,044 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 125: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 13:11:08,063 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 13:11:09,110 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 127: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:11:17,666 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 126 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:11:17,669 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 125 finished +galaxy.model.metadata DEBUG 2024-09-12 13:11:17,746 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 156 +galaxy.model.metadata DEBUG 2024-09-12 13:11:17,747 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 155 +galaxy.jobs INFO 2024-09-12 13:11:17,803 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 126 in /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs INFO 2024-09-12 13:11:17,850 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 125 in /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs DEBUG 2024-09-12 13:11:17,878 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 126 executed (176.287 ms) +galaxy.jobs DEBUG 2024-09-12 13:11:17,915 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 125 executed (211.198 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:11:18,630 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 127 finished +galaxy.model.metadata DEBUG 2024-09-12 13:11:18,700 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 157 +galaxy.jobs INFO 2024-09-12 13:11:18,740 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 127 in /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs DEBUG 2024-09-12 13:11:18,790 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 127 executed (128.651 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:11:19,218 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 128 +tpv.core.entities DEBUG 2024-09-12 13:11:19,268 [pN:job_handler_0,p:9,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={'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_call/lofreq_call/.*, abstract=False, cores=2, mem=8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:11:19,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (128) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:11:19,276 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (128) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:11:19,293 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (128) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:11:19,315 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (128) Working directory for job is: /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs.runners DEBUG 2024-09-12 13:11:19,326 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [128] queued (50.111 ms) +galaxy.jobs.handler INFO 2024-09-12 13:11:19,332 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (128) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:11:19,337 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 128 +galaxy.jobs DEBUG 2024-09-12 13:11:19,456 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [128] prepared (95.260 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:19,457 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:11:19,457 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:19,489 [pN:job_handler_0,p:9,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 2024-09-12 13:11:19,519 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/128/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/128/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/a/1/6/dataset_a160720b-e062-4f72-9197-c5b80f55b0ba.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/galaxy/server/database/objects/c/4/e/dataset_c4ef6f65-10b5-450e-9b43-ef723818cf0b.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/5/b/4/metadata_5b480184-78f8-4bdd-863b-723c6c2687f2.dat' reads.bam.bai && ln -s '/galaxy/server/database/objects/1/a/6/dataset_1a6993a6-b3a3-4df0-a8dc-4484467b2b35.dat' ign0.vcf && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf 'ign0.vcf' --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard] +galaxy.jobs.runners DEBUG 2024-09-12 13:11:19,539 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (128) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/128/working/variants.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/128/working/variants.vcf" "/galaxy/server/database/objects/2/9/7/dataset_297aed2b-d17d-43fa-a7fa-cace109271fc.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:19,552 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:11:19,552 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:19,576 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:11:26,312 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 128: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:11:32,477 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 128 finished +galaxy.model.metadata DEBUG 2024-09-12 13:11:32,543 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 158 +galaxy.util WARNING 2024-09-12 13:11:32,553 [pN:job_handler_0,p:9,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/2/9/7/dataset_297aed2b-d17d-43fa-a7fa-cace109271fc.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/2/9/7/dataset_297aed2b-d17d-43fa-a7fa-cace109271fc.dat' +galaxy.jobs INFO 2024-09-12 13:11:32,587 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 128 in /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs DEBUG 2024-09-12 13:11:32,636 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 128 executed (128.596 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:11:33,812 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 130, 129 +tpv.core.entities DEBUG 2024-09-12 13:11:33,852 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:11:33,853 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (129) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:11:33,868 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (129) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:11:33,886 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (129) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:11:33,906 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (129) Working directory for job is: /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs.runners DEBUG 2024-09-12 13:11:33,914 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [129] queued (45.315 ms) +galaxy.jobs.handler INFO 2024-09-12 13:11:33,918 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (129) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:11:33,923 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 129 +tpv.core.entities DEBUG 2024-09-12 13:11:33,936 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:11:33,936 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (130) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:11:33,944 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (130) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:11:33,963 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (130) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:11:33,997 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (130) Working directory for job is: /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs.runners DEBUG 2024-09-12 13:11:34,006 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [130] queued (61.862 ms) +galaxy.jobs.handler INFO 2024-09-12 13:11:34,012 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (130) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:11:34,018 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 130 +galaxy.jobs DEBUG 2024-09-12 13:11:34,062 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [129] prepared (113.905 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:11:34,097 [pN:job_handler_0,p:9,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' '159:/galaxy/server/database/objects/7/6/0/dataset_760d2696-8cde-4a6d-baca-67e0612593ca_files:/galaxy/server/database/objects/7/6/0/dataset_760d2696-8cde-4a6d-baca-67e0612593ca.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:11:34,115 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:11:34,161 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [130] prepared (117.862 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:11:34,184 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/130/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/130/registry.xml' '/galaxy/server/database/jobs_directory/000/130/upload_params.json' '160:/galaxy/server/database/objects/b/c/9/dataset_bc911942-148e-453d-90e2-c46f6f8a553e_files:/galaxy/server/database/objects/b/c/9/dataset_bc911942-148e-453d-90e2-c46f6f8a553e.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:11:34,199 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (130) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:11:43,695 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 130: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:11:44,721 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:11:50,634 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 130 finished +galaxy.model.metadata DEBUG 2024-09-12 13:11:50,707 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 160 +galaxy.jobs INFO 2024-09-12 13:11:50,753 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 130 in /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs DEBUG 2024-09-12 13:11:50,811 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 130 executed (144.593 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:11:51,609 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 129 finished +galaxy.model.metadata DEBUG 2024-09-12 13:11:51,676 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 159 +galaxy.jobs INFO 2024-09-12 13:11:51,758 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 129 in /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs DEBUG 2024-09-12 13:11:51,812 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 129 executed (173.661 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:11:52,505 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 131 +tpv.core.entities DEBUG 2024-09-12 13:11:52,555 [pN:job_handler_0,p:9,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={'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_call/lofreq_call/.*, abstract=False, cores=2, mem=8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:11:52,556 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (131) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:11:52,562 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (131) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:11:52,581 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (131) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:11:52,603 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (131) Working directory for job is: /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs.runners DEBUG 2024-09-12 13:11:52,614 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [131] queued (51.692 ms) +galaxy.jobs.handler INFO 2024-09-12 13:11:52,619 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (131) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:11:52,624 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 131 +galaxy.jobs DEBUG 2024-09-12 13:11:52,734 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [131] prepared (86.127 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:52,735 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:11:52,735 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:52,764 [pN:job_handler_0,p:9,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 2024-09-12 13:11:52,790 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/131/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/131/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/b/c/9/dataset_bc911942-148e-453d-90e2-c46f6f8a553e.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/galaxy/server/database/objects/7/6/0/dataset_760d2696-8cde-4a6d-baca-67e0612593ca.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/2/5/7/metadata_25717292-b118-40e0-ba4d-2b7dae5213e0.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off] +galaxy.jobs.runners DEBUG 2024-09-12 13:11:52,809 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (131) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/131/working/variants.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/131/working/variants.vcf" "/galaxy/server/database/objects/9/c/5/dataset_9c5336fe-ec44-4181-ac65-9cfc7d68e45f.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:52,823 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:11:52,823 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:11:52,854 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:00,012 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 131: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:12:06,503 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 131 finished +galaxy.model.metadata DEBUG 2024-09-12 13:12:06,572 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 161 +galaxy.util WARNING 2024-09-12 13:12:06,582 [pN:job_handler_0,p:9,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/9/c/5/dataset_9c5336fe-ec44-4181-ac65-9cfc7d68e45f.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/c/5/dataset_9c5336fe-ec44-4181-ac65-9cfc7d68e45f.dat' +galaxy.jobs INFO 2024-09-12 13:12:06,620 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 131 in /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs DEBUG 2024-09-12 13:12:06,670 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 131 executed (133.724 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:12:08,052 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 133, 132 +tpv.core.entities DEBUG 2024-09-12 13:12:08,095 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:12:08,096 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (132) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:12:08,102 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (132) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:12:08,120 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (132) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:12:08,140 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (132) Working directory for job is: /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs.runners DEBUG 2024-09-12 13:12:08,148 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [132] queued (46.593 ms) +galaxy.jobs.handler INFO 2024-09-12 13:12:08,153 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (132) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:12:08,159 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 132 +tpv.core.entities DEBUG 2024-09-12 13:12:08,172 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:12:08,173 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (133) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:12:08,181 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (133) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:12:08,198 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (133) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:12:08,231 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (133) Working directory for job is: /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs.runners DEBUG 2024-09-12 13:12:08,240 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [133] queued (59.092 ms) +galaxy.jobs.handler INFO 2024-09-12 13:12:08,244 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (133) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:12:08,251 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 133 +galaxy.jobs DEBUG 2024-09-12 13:12:08,294 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [132] prepared (108.894 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:12:08,328 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '162:/galaxy/server/database/objects/0/8/e/dataset_08e3cac9-2e3a-4291-b16f-838fb39258c2_files:/galaxy/server/database/objects/0/8/e/dataset_08e3cac9-2e3a-4291-b16f-838fb39258c2.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:08,345 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:12:08,387 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [133] prepared (110.207 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:12:08,412 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/133/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/133/registry.xml' '/galaxy/server/database/jobs_directory/000/133/upload_params.json' '163:/galaxy/server/database/objects/0/a/9/dataset_0a9f0e0a-12ef-4214-b499-654afca7a85a_files:/galaxy/server/database/objects/0/a/9/dataset_0a9f0e0a-12ef-4214-b499-654afca7a85a.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:08,428 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (133) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:12:17,398 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 133: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:12:18,577 [pN:job_handler_0,p:9,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 2024-09-12 13:12:23,926 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 133 finished +galaxy.model.metadata DEBUG 2024-09-12 13:12:23,993 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 163 +galaxy.jobs INFO 2024-09-12 13:12:24,041 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 133 in /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs DEBUG 2024-09-12 13:12:24,098 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 133 executed (141.958 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:12:25,044 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 132 finished +galaxy.model.metadata DEBUG 2024-09-12 13:12:25,118 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 162 +galaxy.jobs INFO 2024-09-12 13:12:25,205 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 132 in /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs DEBUG 2024-09-12 13:12:25,261 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 132 executed (189.388 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:12:26,728 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 134 +tpv.core.entities DEBUG 2024-09-12 13:12:26,776 [pN:job_handler_0,p:9,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={'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_call/lofreq_call/.*, abstract=False, cores=2, mem=8, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:12:26,777 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (134) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:12:26,784 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (134) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:12:26,804 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (134) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:12:26,828 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (134) Working directory for job is: /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs.runners DEBUG 2024-09-12 13:12:26,840 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [134] queued (54.837 ms) +galaxy.jobs.handler INFO 2024-09-12 13:12:26,844 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (134) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:12:26,849 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 134 +galaxy.jobs DEBUG 2024-09-12 13:12:26,955 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [134] prepared (82.378 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:12:26,955 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:12:26,956 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:12:27,187 [pN:job_handler_0,p:9,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 2024-09-12 13:12:27,214 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/134/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/134/outputs/COMMAND_VERSION 2>&1; +ln -s '/galaxy/server/database/objects/0/a/9/dataset_0a9f0e0a-12ef-4214-b499-654afca7a85a.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/galaxy/server/database/objects/0/8/e/dataset_08e3cac9-2e3a-4291-b16f-838fb39258c2.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/3/a/c/metadata_3ace4b26-6eb9-4875-b3fe-8acc9b200551.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:27,232 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (134) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/134/working/variants.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/134/working/variants.vcf" "/galaxy/server/database/objects/1/2/0/dataset_120209da-0d47-4e84-910d-ec4f693ff00e.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:12:27,246 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:12:27,246 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:12:27,269 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:34,873 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 134: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:12:41,391 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 134 finished +galaxy.model.metadata DEBUG 2024-09-12 13:12:41,465 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 164 +galaxy.util WARNING 2024-09-12 13:12:41,476 [pN:job_handler_0,p:9,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/1/2/0/dataset_120209da-0d47-4e84-910d-ec4f693ff00e.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/1/2/0/dataset_120209da-0d47-4e84-910d-ec4f693ff00e.dat' +galaxy.jobs INFO 2024-09-12 13:12:41,515 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 134 in /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs DEBUG 2024-09-12 13:12:41,574 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 134 executed (149.059 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:12:44,313 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 137, 135, 136 +tpv.core.entities DEBUG 2024-09-12 13:12:44,359 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:12:44,360 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (135) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:12:44,366 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (135) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:12:44,385 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (135) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:12:44,408 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (135) Working directory for job is: /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs.runners DEBUG 2024-09-12 13:12:44,418 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [135] queued (51.928 ms) +galaxy.jobs.handler INFO 2024-09-12 13:12:44,422 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (135) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:12:44,430 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 135 +tpv.core.entities DEBUG 2024-09-12 13:12:44,441 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:12:44,442 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (136) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:12:44,448 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (136) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:12:44,469 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (136) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:12:44,508 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (136) Working directory for job is: /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs.runners DEBUG 2024-09-12 13:12:44,518 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [136] queued (69.799 ms) +galaxy.jobs.handler INFO 2024-09-12 13:12:44,523 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (136) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:12:44,532 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 136 +tpv.core.entities DEBUG 2024-09-12 13:12:44,553 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:12:44,553 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (137) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:12:44,563 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (137) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:12:44,587 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (137) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:12:44,608 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [135] prepared (149.496 ms) +galaxy.jobs DEBUG 2024-09-12 13:12:44,636 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (137) Working directory for job is: /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs.runners DEBUG 2024-09-12 13:12:44,645 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [137] queued (81.906 ms) +galaxy.jobs.handler INFO 2024-09-12 13:12:44,650 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (137) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:12:44,660 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 137 +galaxy.jobs.command_factory INFO 2024-09-12 13:12:44,661 [pN:job_handler_0,p:9,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' '165:/galaxy/server/database/objects/2/0/3/dataset_2031316f-3985-4d58-8ecf-b985dcebff03_files:/galaxy/server/database/objects/2/0/3/dataset_2031316f-3985-4d58-8ecf-b985dcebff03.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:44,703 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:12:44,718 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [136] prepared (148.256 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:12:44,768 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/136/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/136/registry.xml' '/galaxy/server/database/jobs_directory/000/136/upload_params.json' '166:/galaxy/server/database/objects/a/8/d/dataset_a8d0bc7c-240a-48b0-ab29-652f0d7a6797_files:/galaxy/server/database/objects/a/8/d/dataset_a8d0bc7c-240a-48b0-ab29-652f0d7a6797.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:44,791 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (136) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:12:44,836 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [137] prepared (142.734 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:12:44,860 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/137/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/137/registry.xml' '/galaxy/server/database/jobs_directory/000/137/upload_params.json' '167:/galaxy/server/database/objects/8/a/8/dataset_8a8438d1-3af6-4f3f-8507-1e8f58316b06_files:/galaxy/server/database/objects/8/a/8/dataset_8a8438d1-3af6-4f3f-8507-1e8f58316b06.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:12:44,879 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (137) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:12:54,573 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 135: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:12:54,611 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 13:12:54,629 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 137: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 13:13:04,877 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 135 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:13:04,913 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 136 finished +galaxy.model.metadata DEBUG 2024-09-12 13:13:04,981 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 165 +galaxy.model.metadata DEBUG 2024-09-12 13:13:05,027 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 166 +galaxy.jobs INFO 2024-09-12 13:13:05,046 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 135 in /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs INFO 2024-09-12 13:13:05,085 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 136 in /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs DEBUG 2024-09-12 13:13:05,135 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 135 executed (228.315 ms) +galaxy.jobs DEBUG 2024-09-12 13:13:05,173 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 136 executed (200.951 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:13:05,198 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 137 finished +galaxy.model.metadata DEBUG 2024-09-12 13:13:05,276 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 167 +galaxy.jobs INFO 2024-09-12 13:13:05,323 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 137 in /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs DEBUG 2024-09-12 13:13:05,382 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 137 executed (144.559 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:13:06,625 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 138 +tpv.core.entities DEBUG 2024-09-12 13:13:06,678 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:13:06,679 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (138) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:13:06,687 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (138) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:13:06,706 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (138) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:13:06,728 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (138) Working directory for job is: /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs.runners DEBUG 2024-09-12 13:13:06,738 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [138] queued (51.190 ms) +galaxy.jobs.handler INFO 2024-09-12 13:13:06,744 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (138) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:13:06,749 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 138 +galaxy.jobs DEBUG 2024-09-12 13:13:06,864 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [138] prepared (91.998 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:06,864 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:13:06,865 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:13:07,074 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:13:07,100 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/138/tool_script.sh] for tool command [ivar version | grep version > /galaxy/server/database/jobs_directory/000/138/outputs/COMMAND_VERSION 2>&1; +ivar getmasked -i '/galaxy/server/database/objects/2/0/3/dataset_2031316f-3985-4d58-8ecf-b985dcebff03.dat' -b '/galaxy/server/database/objects/a/8/d/dataset_a8d0bc7c-240a-48b0-ab29-652f0d7a6797.dat' -f '/galaxy/server/database/objects/8/a/8/dataset_8a8438d1-3af6-4f3f-8507-1e8f58316b06.dat' -p masked_primers] +galaxy.jobs.runners DEBUG 2024-09-12 13:13:07,118 [pN:job_handler_0,p:9,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; +if [ -f "/galaxy/server/database/jobs_directory/000/138/working/masked_primers.txt" ] ; then cp "/galaxy/server/database/jobs_directory/000/138/working/masked_primers.txt" "/galaxy/server/database/objects/4/9/c/dataset_49cf346a-e35d-4591-b87a-bcca8b09a449.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:07,133 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:13:07,134 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0: mulled-v2-98ddb1f3cf1349cc3c286418d2895004e1791819:fae61fa977b1364550a2df32f067b432629eced7 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:07,158 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-98ddb1f3cf1349cc3c286418d2895004e1791819:fae61fa977b1364550a2df32f067b432629eced7-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:13:14,830 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 138: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:13:21,348 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 138 finished +galaxy.model.metadata DEBUG 2024-09-12 13:13:21,423 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 168 +galaxy.util WARNING 2024-09-12 13:13:21,431 [pN:job_handler_0,p:9,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/c/dataset_49cf346a-e35d-4591-b87a-bcca8b09a449.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/c/dataset_49cf346a-e35d-4591-b87a-bcca8b09a449.dat' +galaxy.jobs INFO 2024-09-12 13:13:21,467 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 138 in /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs DEBUG 2024-09-12 13:13:21,524 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 138 executed (144.495 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:13:24,220 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 139 +tpv.core.entities DEBUG 2024-09-12 13:13:24,262 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:13:24,263 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (139) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:13:24,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (139) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:13:24,289 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (139) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:13:24,311 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (139) Working directory for job is: /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs.runners DEBUG 2024-09-12 13:13:24,319 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [139] queued (49.440 ms) +galaxy.jobs.handler INFO 2024-09-12 13:13:24,323 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (139) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:13:24,328 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 139 +galaxy.jobs DEBUG 2024-09-12 13:13:24,468 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [139] prepared (115.041 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:13:24,494 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/139/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/139/registry.xml' '/galaxy/server/database/jobs_directory/000/139/upload_params.json' '169:/galaxy/server/database/objects/f/2/f/dataset_f2f6526b-1c0c-4b3b-96b2-2387f3fb4fe6_files:/galaxy/server/database/objects/f/2/f/dataset_f2f6526b-1c0c-4b3b-96b2-2387f3fb4fe6.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:13:24,511 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:13:34,077 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 139: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:13:40,579 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 139 finished +galaxy.model.metadata DEBUG 2024-09-12 13:13:40,648 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 169 +galaxy.jobs INFO 2024-09-12 13:13:40,697 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 139 in /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs DEBUG 2024-09-12 13:13:40,755 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 139 executed (144.827 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:13:41,821 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 140 +tpv.core.entities DEBUG 2024-09-12 13:13:41,870 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:13:41,871 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (140) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:13:41,877 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (140) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:13:41,897 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (140) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:13:41,916 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (140) Working directory for job is: /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs.runners DEBUG 2024-09-12 13:13:41,925 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [140] queued (48.117 ms) +galaxy.jobs.handler INFO 2024-09-12 13:13:41,930 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (140) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:13:41,935 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 140 +galaxy.security.object_wrapper WARNING 2024-09-12 13:13:42,111 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Unable to create dynamic subclass SafeStringWrapper__galaxy.model.metadata.None__NoneType__NotImplementedType__Number__SafeStringWrapper__ToolParameterValueWrapper__bool__bytearray__ellipsis for , {'dbkey': '?', 'data_lines': 2881, 'sequences': 1}: type() doesn't support MRO entry resolution; use types.new_class() +galaxy.jobs DEBUG 2024-09-12 13:13:42,170 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [140] prepared (211.588 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:42,171 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:13:42,171 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:42,380 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:13:42,406 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/140/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/140/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36_files && cp /galaxy/server/database/jobs_directory/000/140/configs/tmp0zdx0ef8 /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36_files /galaxy/server/database/jobs_directory/000/140/configs/tmp0zdx0ef8 && cp /galaxy/server/database/jobs_directory/000/140/configs/tmp1mv6jzvr /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36.dat; cp /galaxy/server/database/jobs_directory/000/140/configs/tmp0zdx0ef8 /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:13:42,423 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (140) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:42,436 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:13:42,436 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:13:42,458 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:09,657 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 140: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-12 13:14:16,009 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 140 finished +galaxy.model.metadata DEBUG 2024-09-12 13:14:16,106 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 170 +galaxy.util WARNING 2024-09-12 13:14:16,117 [pN:job_handler_0,p:9,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/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36.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/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36.dat' +galaxy.jobs INFO 2024-09-12 13:14:16,156 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 140 in /galaxy/server/database/jobs_directory/000/140 +galaxy.objectstore CRITICAL 2024-09-12 13:14:16,204 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmp0zdx0ef8' +galaxy.jobs DEBUG 2024-09-12 13:14:16,204 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 140 executed (162.105 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:14:17,917 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 141 +tpv.core.entities DEBUG 2024-09-12 13:14:17,960 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:14:17,961 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (141) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:14:17,967 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (141) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:14:17,986 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (141) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:14:18,007 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (141) Working directory for job is: /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs.runners DEBUG 2024-09-12 13:14:18,018 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [141] queued (50.493 ms) +galaxy.jobs.handler INFO 2024-09-12 13:14:18,022 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (141) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:14:18,027 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 141 +galaxy.jobs DEBUG 2024-09-12 13:14:18,165 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [141] prepared (112.600 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:14:18,191 [pN:job_handler_0,p:9,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' '171:/galaxy/server/database/objects/f/4/d/dataset_f4d527b9-8f60-4a69-a540-25737016bd88_files:/galaxy/server/database/objects/f/4/d/dataset_f4d527b9-8f60-4a69-a540-25737016bd88.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:18,207 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:14:28,985 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 141: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:14:35,337 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 141 finished +galaxy.model.metadata DEBUG 2024-09-12 13:14:35,410 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 171 +galaxy.jobs INFO 2024-09-12 13:14:35,483 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 141 in /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs DEBUG 2024-09-12 13:14:35,562 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 141 executed (192.906 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:14:36,611 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 142 +tpv.core.entities DEBUG 2024-09-12 13:14:36,659 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:14:36,659 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (142) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:14:36,666 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (142) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:14:36,685 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (142) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:14:36,708 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (142) Working directory for job is: /galaxy/server/database/jobs_directory/000/142 +galaxy.jobs.runners DEBUG 2024-09-12 13:14:36,719 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [142] queued (52.910 ms) +galaxy.jobs.handler INFO 2024-09-12 13:14:36,724 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (142) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:14:36,730 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 142 +galaxy.jobs DEBUG 2024-09-12 13:14:36,863 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [142] prepared (108.098 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:14:36,864 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:14:36,864 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:14:36,889 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:14:36,915 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/142/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/142/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370_files && cp /galaxy/server/database/jobs_directory/000/142/configs/tmp8ze933lk /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370_files /galaxy/server/database/jobs_directory/000/142/configs/tmp8ze933lk && cp /galaxy/server/database/jobs_directory/000/142/configs/tmp0e8diaxb /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370.dat; cp /galaxy/server/database/jobs_directory/000/142/configs/tmp8ze933lk /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:36,931 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (142) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:14:36,945 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:14:36,945 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:14:36,967 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:42,125 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 142: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:14:48,453 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 142 finished +galaxy.model.metadata DEBUG 2024-09-12 13:14:48,550 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 172 +galaxy.util WARNING 2024-09-12 13:14:48,560 [pN:job_handler_0,p:9,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/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370.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/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370.dat' +galaxy.jobs INFO 2024-09-12 13:14:48,594 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 142 in /galaxy/server/database/jobs_directory/000/142 +galaxy.objectstore CRITICAL 2024-09-12 13:14:48,638 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmp8ze933lk' +galaxy.jobs DEBUG 2024-09-12 13:14:48,638 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 142 executed (153.237 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:14:50,066 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 144, 143 +tpv.core.entities DEBUG 2024-09-12 13:14:50,110 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:14:50,110 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (143) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:14:50,118 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (143) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:14:50,137 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (143) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:14:50,157 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (143) Working directory for job is: /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs.runners DEBUG 2024-09-12 13:14:50,165 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [143] queued (47.493 ms) +galaxy.jobs.handler INFO 2024-09-12 13:14:50,169 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (143) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:14:50,175 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 143 +tpv.core.entities DEBUG 2024-09-12 13:14:50,188 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:14:50,189 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (144) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:14:50,197 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (144) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:14:50,217 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (144) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:14:50,256 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (144) Working directory for job is: /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs.runners DEBUG 2024-09-12 13:14:50,264 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [144] queued (66.653 ms) +galaxy.jobs.handler INFO 2024-09-12 13:14:50,269 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (144) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:14:50,275 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 144 +galaxy.jobs DEBUG 2024-09-12 13:14:50,325 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [143] prepared (122.844 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:14:50,364 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '173:/galaxy/server/database/objects/e/0/d/dataset_e0d7f460-5be5-47f2-82b6-3f73259283fe_files:/galaxy/server/database/objects/e/0/d/dataset_e0d7f460-5be5-47f2-82b6-3f73259283fe.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:50,401 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:14:50,423 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [144] prepared (120.228 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:14:50,449 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/144/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/144/registry.xml' '/galaxy/server/database/jobs_directory/000/144/upload_params.json' '174:/galaxy/server/database/objects/2/7/d/dataset_27d577ab-e353-4c22-8057-3c4380846bc5_files:/galaxy/server/database/objects/2/7/d/dataset_27d577ab-e353-4c22-8057-3c4380846bc5.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:50,465 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (144) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.handler DEBUG 2024-09-12 13:14:51,272 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 145 +tpv.core.entities DEBUG 2024-09-12 13:14:51,316 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:14:51,317 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (145) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:14:51,324 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (145) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:14:51,346 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (145) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:14:51,366 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (145) Working directory for job is: /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs.runners DEBUG 2024-09-12 13:14:51,374 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [145] queued (49.461 ms) +galaxy.jobs.handler INFO 2024-09-12 13:14:51,379 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (145) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:14:51,384 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 145 +galaxy.jobs DEBUG 2024-09-12 13:14:51,512 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [145] prepared (104.355 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:14:51,537 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '175:/galaxy/server/database/objects/8/a/9/dataset_8a9afc89-cbd5-4389-9494-d3784d7b6fd0_files:/galaxy/server/database/objects/8/a/9/dataset_8a9afc89-cbd5-4389-9494-d3784d7b6fd0.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:14:51,553 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 ERROR 2024-09-12 13:14:59,675 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-kphl5 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-kphl5": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:14:59,749 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (143/gxy-kphl5) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-12 13:14:59,894 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 144: 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 2024-09-12 13:15:00,616 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 146 +tpv.core.entities DEBUG 2024-09-12 13:15:00,666 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:00,667 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (146) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:00,674 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (146) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:00,694 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (146) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:00,714 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (146) Working directory for job is: /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:00,729 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [146] queued (54.301 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:00,734 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (146) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:00,739 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 146 +galaxy.jobs DEBUG 2024-09-12 13:15:00,893 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [146] prepared (128.495 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:00,918 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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' '176:/galaxy/server/database/objects/d/3/0/dataset_d30b799e-3ce2-4da4-87c0-800c9ed1aea9_files:/galaxy/server/database/objects/d/3/0/dataset_d30b799e-3ce2-4da4-87c0-800c9ed1aea9.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:00,935 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:15:00,968 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 145: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.handler DEBUG 2024-09-12 13:15:01,738 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 148, 149, 147 +tpv.core.entities DEBUG 2024-09-12 13:15:01,812 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:01,813 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (147) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:01,852 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (147) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:01,876 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (147) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:01,897 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (147) Working directory for job is: /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:01,909 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [147] queued (56.768 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:01,914 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (147) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:01,921 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 147 +tpv.core.entities DEBUG 2024-09-12 13:15:01,964 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:01,965 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (148) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:01,975 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (148) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:01,997 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (148) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:02,079 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (148) Working directory for job is: /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:02,090 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [148] queued (115.314 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:02,096 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (148) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:02,105 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 148 +tpv.core.entities DEBUG 2024-09-12 13:15:02,172 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:02,172 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (149) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:02,182 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (149) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:02,252 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (149) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:02,266 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [147] prepared (284.972 ms) +galaxy.jobs DEBUG 2024-09-12 13:15:02,310 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (149) Working directory for job is: /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs.command_factory INFO 2024-09-12 13:15:02,355 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/147/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/147/registry.xml' '/galaxy/server/database/jobs_directory/000/147/upload_params.json' '177:/galaxy/server/database/objects/8/e/9/dataset_8e975945-148a-4234-9c24-188021171e22_files:/galaxy/server/database/objects/8/e/9/dataset_8e975945-148a-4234-9c24-188021171e22.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:02,357 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [149] queued (175.196 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:02,363 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (149) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 13:15:02,379 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:15:02,452 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [148] prepared (273.031 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:02,478 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 149 +galaxy.jobs.command_factory INFO 2024-09-12 13:15:02,487 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/148/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/148/registry.xml' '/galaxy/server/database/jobs_directory/000/148/upload_params.json' '178:/galaxy/server/database/objects/e/1/b/dataset_e1b7ddd4-4ccc-45c0-8b31-4355ba54a9b6_files:/galaxy/server/database/objects/e/1/b/dataset_e1b7ddd4-4ccc-45c0-8b31-4355ba54a9b6.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:02,505 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (148) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:15:02,697 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [149] prepared (184.643 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:02,724 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/149/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/149/registry.xml' '/galaxy/server/database/jobs_directory/000/149/upload_params.json' '179:/galaxy/server/database/objects/d/e/5/dataset_de560582-71d2-4146-bcfa-d16c99a9094b_files:/galaxy/server/database/objects/d/e/5/dataset_de560582-71d2-4146-bcfa-d16c99a9094b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:02,759 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (149) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-12 13:15:03,367 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 151, 150, 152, 153 +tpv.core.entities DEBUG 2024-09-12 13:15:03,415 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:03,416 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (150) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:03,423 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (150) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:03,470 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (150) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:03,493 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (150) Working directory for job is: /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:03,504 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [150] queued (81.229 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:03,510 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (150) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:03,517 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 150 +tpv.core.entities DEBUG 2024-09-12 13:15:03,557 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:03,558 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (151) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:03,565 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (151) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:03,589 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (151) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:03,666 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (151) Working directory for job is: /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:03,677 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [151] queued (111.183 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:03,684 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (151) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:03,692 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 151 +tpv.core.entities DEBUG 2024-09-12 13:15:03,760 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:03,761 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (152) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:03,772 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (152) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:03,801 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (152) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:03,811 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [150] prepared (238.345 ms) +galaxy.jobs DEBUG 2024-09-12 13:15:03,879 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (152) Working directory for job is: /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:03,890 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [152] queued (118.463 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:03,894 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '180:/galaxy/server/database/objects/8/4/6/dataset_84699dfc-7ae5-4799-8bec-98ae16d599c9_files:/galaxy/server/database/objects/8/4/6/dataset_84699dfc-7ae5-4799-8bec-98ae16d599c9.dat'] +galaxy.jobs.handler INFO 2024-09-12 13:15:03,899 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (152) Job dispatched +galaxy.jobs.runners DEBUG 2024-09-12 13:15:03,960 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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" +tpv.core.entities DEBUG 2024-09-12 13:15:03,970 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:03,971 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (153) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:03,983 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (153) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:04,009 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [151] prepared (236.080 ms) +galaxy.jobs DEBUG 2024-09-12 13:15:04,056 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (153) Persisting job destination (destination id: k8s) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:04,080 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 152 +galaxy.jobs.command_factory INFO 2024-09-12 13:15:04,082 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/151/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/151/registry.xml' '/galaxy/server/database/jobs_directory/000/151/upload_params.json' '181:/galaxy/server/database/objects/a/8/1/dataset_a812c6a5-0950-4de6-aea7-a50af2a6529e_files:/galaxy/server/database/objects/a/8/1/dataset_a812c6a5-0950-4de6-aea7-a50af2a6529e.dat'] +galaxy.jobs DEBUG 2024-09-12 13:15:04,093 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (153) Working directory for job is: /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:04,109 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [153] queued (125.880 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:15:04,112 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (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; sh -c "exit $return_code" +galaxy.jobs.handler INFO 2024-09-12 13:15:04,116 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (153) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:04,281 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 153 +galaxy.jobs DEBUG 2024-09-12 13:15:04,359 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [152] prepared (239.432 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:04,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/152/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/152/registry.xml' '/galaxy/server/database/jobs_directory/000/152/upload_params.json' '182:/galaxy/server/database/objects/3/6/7/dataset_3675266f-4d20-4c2d-9482-98656abf6859_files:/galaxy/server/database/objects/3/6/7/dataset_3675266f-4d20-4c2d-9482-98656abf6859.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:04,486 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (152) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:15:04,595 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [153] prepared (284.964 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:04,668 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/153/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/153/registry.xml' '/galaxy/server/database/jobs_directory/000/153/upload_params.json' '183:/galaxy/server/database/objects/0/9/1/dataset_09149cb4-bb95-4819-8da7-353524d518a5_files:/galaxy/server/database/objects/0/9/1/dataset_09149cb4-bb95-4819-8da7-353524d518a5.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:04,706 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (153) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:15:09,056 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 144 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:09,143 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 174 +galaxy.jobs INFO 2024-09-12 13:15:09,198 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 144 in /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs DEBUG 2024-09-12 13:15:09,262 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 144 executed (162.961 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:15:10,131 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 145 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:10,225 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 175 +galaxy.jobs INFO 2024-09-12 13:15:10,272 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 145 in /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs DEBUG 2024-09-12 13:15:10,348 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 145 executed (174.228 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:15:11,412 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 146: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:15:13,776 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 13:15:13,808 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 148: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:15:13,862 [pN:job_handler_0,p:9,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 13:15:23,275 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 146 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:23,406 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 176 +galaxy.jobs INFO 2024-09-12 13:15:23,497 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 146 in /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs DEBUG 2024-09-12 13:15:23,601 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 146 executed (239.730 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:15:24,055 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 150: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:15:27,559 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 148 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:15:27,685 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 147 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:15:27,689 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 149 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:27,699 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 178 +galaxy.jobs INFO 2024-09-12 13:15:27,797 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 148 in /galaxy/server/database/jobs_directory/000/148 +galaxy.model.metadata DEBUG 2024-09-12 13:15:27,821 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 177 +galaxy.model.metadata DEBUG 2024-09-12 13:15:27,822 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 179 +galaxy.jobs INFO 2024-09-12 13:15:27,883 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 147 in /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs INFO 2024-09-12 13:15:27,888 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 149 in /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs DEBUG 2024-09-12 13:15:27,906 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 148 executed (310.447 ms) +galaxy.jobs DEBUG 2024-09-12 13:15:27,957 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 147 executed (191.753 ms) +galaxy.jobs DEBUG 2024-09-12 13:15:27,964 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 149 executed (195.619 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:15:28,167 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 151: 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-12 13:15:28,308 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 153: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:15:28,380 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:15:37,954 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 150 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:38,072 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 180 +galaxy.jobs INFO 2024-09-12 13:15:38,168 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 150 in /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs DEBUG 2024-09-12 13:15:38,275 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 150 executed (288.742 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:15:40,802 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 153 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:15:40,808 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 151 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:40,909 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 183 +galaxy.model.metadata DEBUG 2024-09-12 13:15:40,921 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 181 +galaxy.jobs INFO 2024-09-12 13:15:40,972 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 153 in /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs INFO 2024-09-12 13:15:40,986 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 151 in /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:40,997 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 152 finished +galaxy.jobs DEBUG 2024-09-12 13:15:41,065 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 153 executed (201.279 ms) +galaxy.model.metadata DEBUG 2024-09-12 13:15:41,086 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 182 +galaxy.jobs DEBUG 2024-09-12 13:15:41,088 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 151 executed (214.201 ms) +galaxy.jobs INFO 2024-09-12 13:15:41,147 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 152 in /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs DEBUG 2024-09-12 13:15:41,213 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 152 executed (182.066 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:15:42,531 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 154 +tpv.core.entities DEBUG 2024-09-12 13:15:42,608 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:42,609 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (154) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:42,618 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (154) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:42,639 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (154) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:42,663 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (154) Working directory for job is: /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:42,682 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [154] queued (64.384 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:42,687 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (154) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:42,692 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 154 +galaxy.jobs DEBUG 2024-09-12 13:15:42,998 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [154] prepared (280.032 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:15:42,998 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:15:42,999 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:15:43,026 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:15:43,054 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/154/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/154/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8_files && cp /galaxy/server/database/jobs_directory/000/154/configs/tmpl8s3cdk_ /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8_files /galaxy/server/database/jobs_directory/000/154/configs/tmpl8s3cdk_ && cp /galaxy/server/database/jobs_directory/000/154/configs/tmpv5z9yaqs /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8.dat; cp /galaxy/server/database/jobs_directory/000/154/configs/tmpl8s3cdk_ /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:43,072 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (154) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:15:43,087 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:15:43,087 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:15:43,112 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:50,524 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 154: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:15:57,012 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 154 finished +galaxy.model.metadata DEBUG 2024-09-12 13:15:57,131 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 184 +galaxy.util WARNING 2024-09-12 13:15:57,146 [pN:job_handler_0,p:9,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/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8.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/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8.dat' +galaxy.jobs INFO 2024-09-12 13:15:57,182 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 154 in /galaxy/server/database/jobs_directory/000/154 +galaxy.objectstore CRITICAL 2024-09-12 13:15:57,227 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpv5z9yaqs' +galaxy.jobs DEBUG 2024-09-12 13:15:57,227 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 154 executed (181.627 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:15:59,167 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 155, 156 +tpv.core.entities DEBUG 2024-09-12 13:15:59,208 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:59,209 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (155) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:59,215 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (155) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:59,232 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (155) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:59,249 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (155) Working directory for job is: /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:59,257 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [155] queued (42.273 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:59,261 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (155) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:59,267 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 155 +tpv.core.entities DEBUG 2024-09-12 13:15:59,280 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:15:59,281 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (156) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:15:59,288 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (156) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:15:59,307 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (156) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:15:59,338 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (156) Working directory for job is: /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs.runners DEBUG 2024-09-12 13:15:59,347 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [156] queued (58.569 ms) +galaxy.jobs.handler INFO 2024-09-12 13:15:59,351 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (156) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:15:59,356 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 156 +galaxy.jobs DEBUG 2024-09-12 13:15:59,410 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [155] prepared (117.567 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:59,442 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/155/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/155/registry.xml' '/galaxy/server/database/jobs_directory/000/155/upload_params.json' '185:/galaxy/server/database/objects/5/3/3/dataset_5335f8c6-dee0-4669-8370-99caba3e7062_files:/galaxy/server/database/objects/5/3/3/dataset_5335f8c6-dee0-4669-8370-99caba3e7062.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:59,459 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:15:59,496 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [156] prepared (113.682 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:15:59,521 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/156/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/156/registry.xml' '/galaxy/server/database/jobs_directory/000/156/upload_params.json' '186:/galaxy/server/database/objects/1/2/8/dataset_12886cb2-dc6a-49ec-8871-d685f79bb766_files:/galaxy/server/database/objects/1/2/8/dataset_12886cb2-dc6a-49ec-8871-d685f79bb766.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:15:59,535 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (156) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:16:09,905 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 155: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:16:09,931 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 156: 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 2024-09-12 13:16:16,897 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 156 finished +galaxy.jobs.runners DEBUG 2024-09-12 13:16:16,936 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 155 finished +galaxy.model.metadata DEBUG 2024-09-12 13:16:16,970 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 186 +galaxy.model.metadata DEBUG 2024-09-12 13:16:17,018 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 185 +galaxy.jobs INFO 2024-09-12 13:16:17,031 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 156 in /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs INFO 2024-09-12 13:16:17,066 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 155 in /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs DEBUG 2024-09-12 13:16:17,104 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 156 executed (176.851 ms) +galaxy.jobs DEBUG 2024-09-12 13:16:17,135 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 155 executed (165.694 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:16:17,907 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 157 +tpv.core.entities DEBUG 2024-09-12 13:16:17,955 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:16:17,956 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (157) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:16:17,963 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (157) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:16:17,981 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (157) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:16:18,003 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (157) Working directory for job is: /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs.runners DEBUG 2024-09-12 13:16:18,014 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [157] queued (51.642 ms) +galaxy.jobs.handler INFO 2024-09-12 13:16:18,019 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (157) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:16:18,025 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 157 +galaxy.jobs DEBUG 2024-09-12 13:16:18,177 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [157] prepared (126.914 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:18,177 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:16:18,178 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:18,202 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:16:18,229 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/157/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/157/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751_files && cp /galaxy/server/database/jobs_directory/000/157/configs/tmp6o_mfd9h /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751_files /galaxy/server/database/jobs_directory/000/157/configs/tmp6o_mfd9h && cp /galaxy/server/database/jobs_directory/000/157/configs/tmpcdut7beg /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751.dat; cp /galaxy/server/database/jobs_directory/000/157/configs/tmp6o_mfd9h /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:16:18,245 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (157) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:18,257 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:16:18,258 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:18,278 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:16:26,263 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 157: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-12 13:16:32,540 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 157 finished +galaxy.model.metadata DEBUG 2024-09-12 13:16:32,724 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 187 +galaxy.util WARNING 2024-09-12 13:16:32,753 [pN:job_handler_0,p:9,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/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751.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/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751.dat' +galaxy.jobs INFO 2024-09-12 13:16:32,787 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 157 in /galaxy/server/database/jobs_directory/000/157 +galaxy.objectstore CRITICAL 2024-09-12 13:16:32,835 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmpcdut7beg' +galaxy.jobs DEBUG 2024-09-12 13:16:32,835 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 157 executed (260.552 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:16:34,449 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 159, 158 +tpv.core.entities DEBUG 2024-09-12 13:16:34,496 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:16:34,497 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (158) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:16:34,504 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (158) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:16:34,525 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (158) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:16:34,546 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (158) Working directory for job is: /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs.runners DEBUG 2024-09-12 13:16:34,555 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [158] queued (50.237 ms) +galaxy.jobs.handler INFO 2024-09-12 13:16:34,559 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (158) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:16:34,565 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 158 +tpv.core.entities DEBUG 2024-09-12 13:16:34,579 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:16:34,580 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (159) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:16:34,588 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (159) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:16:34,608 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (159) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:16:34,645 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (159) Working directory for job is: /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs.runners DEBUG 2024-09-12 13:16:34,655 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [159] queued (66.767 ms) +galaxy.jobs.handler INFO 2024-09-12 13:16:34,660 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (159) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:16:34,666 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 159 +galaxy.jobs DEBUG 2024-09-12 13:16:34,720 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [158] prepared (126.599 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:16:34,755 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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' '188:/galaxy/server/database/objects/f/b/7/dataset_fb7e893a-b842-4fcf-b154-cd4a5a16fa9b_files:/galaxy/server/database/objects/f/b/7/dataset_fb7e893a-b842-4fcf-b154-cd4a5a16fa9b.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:16:34,790 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs DEBUG 2024-09-12 13:16:34,820 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [159] prepared (124.928 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:16:34,845 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/159/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/159/registry.xml' '/galaxy/server/database/jobs_directory/000/159/upload_params.json' '189:/galaxy/server/database/objects/1/2/e/dataset_12e7fdf7-a36b-460d-aee8-22d13fd4d43f_files:/galaxy/server/database/objects/1/2/e/dataset_12e7fdf7-a36b-460d-aee8-22d13fd4d43f.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:16:34,860 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (159) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:16:44,675 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 158: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:16:44,709 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] 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 2024-09-12 13:16:51,619 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 158 finished +galaxy.model.metadata DEBUG 2024-09-12 13:16:51,687 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 188 +galaxy.jobs.runners DEBUG 2024-09-12 13:16:51,697 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 159 finished +galaxy.jobs INFO 2024-09-12 13:16:51,738 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 158 in /galaxy/server/database/jobs_directory/000/158 +galaxy.model.metadata DEBUG 2024-09-12 13:16:51,773 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 189 +galaxy.jobs DEBUG 2024-09-12 13:16:51,815 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 158 executed (165.364 ms) +galaxy.jobs INFO 2024-09-12 13:16:51,821 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 159 in /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs DEBUG 2024-09-12 13:16:51,886 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 159 executed (146.492 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:16:52,135 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 160 +tpv.core.entities DEBUG 2024-09-12 13:16:52,183 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:16:52,184 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (160) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:16:52,190 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (160) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:16:52,209 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (160) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:16:52,231 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (160) Working directory for job is: /galaxy/server/database/jobs_directory/000/160 +galaxy.jobs.runners DEBUG 2024-09-12 13:16:52,241 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [160] queued (50.941 ms) +galaxy.jobs.handler INFO 2024-09-12 13:16:52,246 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (160) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:16:52,251 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 160 +galaxy.jobs DEBUG 2024-09-12 13:16:52,384 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [160] prepared (111.640 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:52,384 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:16:52,385 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:52,409 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:16:52,432 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/160/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/160/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41_files && cp /galaxy/server/database/jobs_directory/000/160/configs/tmpxs4sin6v /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41_files /galaxy/server/database/jobs_directory/000/160/configs/tmpxs4sin6v && cp /galaxy/server/database/jobs_directory/000/160/configs/tmpt06hjvjp /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41.dat; cp /galaxy/server/database/jobs_directory/000/160/configs/tmpxs4sin6v /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:16:52,449 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (160) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:52,462 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:16:52,462 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:16:52,482 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:16:57,904 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 160: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:17:04,220 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 160 finished +galaxy.model.metadata DEBUG 2024-09-12 13:17:04,311 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 190 +galaxy.util WARNING 2024-09-12 13:17:04,323 [pN:job_handler_0,p:9,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/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41.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/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41.dat' +galaxy.jobs INFO 2024-09-12 13:17:04,357 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 160 in /galaxy/server/database/jobs_directory/000/160 +galaxy.objectstore CRITICAL 2024-09-12 13:17:04,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpxs4sin6v' +galaxy.jobs DEBUG 2024-09-12 13:17:04,407 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 160 executed (154.763 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:17:05,591 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 161 +tpv.core.entities DEBUG 2024-09-12 13:17:05,634 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:17:05,635 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (161) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:17:05,655 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (161) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:17:05,676 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (161) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:17:05,699 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (161) Working directory for job is: /galaxy/server/database/jobs_directory/000/161 +galaxy.jobs.runners DEBUG 2024-09-12 13:17:05,709 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [161] queued (53.105 ms) +galaxy.jobs.handler INFO 2024-09-12 13:17:05,713 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (161) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:05,719 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 161 +galaxy.jobs DEBUG 2024-09-12 13:17:05,843 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [161] prepared (100.876 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:17:05,865 [pN:job_handler_0,p:9,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' '191:/galaxy/server/database/objects/7/e/e/dataset_7ee98eb7-428a-4eb2-bbcc-e05132669719_files:/galaxy/server/database/objects/7/e/e/dataset_7ee98eb7-428a-4eb2-bbcc-e05132669719.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:05,880 [pN:job_handler_0,p:9,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.handler DEBUG 2024-09-12 13:17:06,717 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 162 +tpv.core.entities DEBUG 2024-09-12 13:17:06,765 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:17:06,766 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (162) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:17:06,773 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (162) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:17:06,790 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (162) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:17:06,809 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (162) Working directory for job is: /galaxy/server/database/jobs_directory/000/162 +galaxy.jobs.runners DEBUG 2024-09-12 13:17:06,817 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [162] queued (44.247 ms) +galaxy.jobs.handler INFO 2024-09-12 13:17:06,822 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (162) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:06,827 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 162 +galaxy.jobs DEBUG 2024-09-12 13:17:06,963 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [162] prepared (111.738 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:17:06,987 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '192:/galaxy/server/database/objects/6/8/0/dataset_68083c16-586b-4815-9082-fd567885f88c_files:/galaxy/server/database/objects/6/8/0/dataset_68083c16-586b-4815-9082-fd567885f88c.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:07,001 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 ERROR 2024-09-12 13:17:15,218 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-hrbwr + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-hrbwr": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:15,259 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (161/gxy-hrbwr) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-12 13:17:15,410 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] 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 2024-09-12 13:17:16,046 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 163 +tpv.core.entities DEBUG 2024-09-12 13:17:16,103 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:17:16,104 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (163) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:17:16,111 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (163) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:17:16,130 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (163) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:17:16,150 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (163) Working directory for job is: /galaxy/server/database/jobs_directory/000/163 +galaxy.jobs.runners DEBUG 2024-09-12 13:17:16,160 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [163] queued (48.517 ms) +galaxy.jobs.handler INFO 2024-09-12 13:17:16,164 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (163) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:16,169 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 163 +galaxy.jobs DEBUG 2024-09-12 13:17:16,291 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [163] prepared (100.241 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:17:16,314 [pN:job_handler_0,p:9,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' '193:/galaxy/server/database/objects/7/5/e/dataset_75e6bc1e-c1cd-4f26-a0a0-7653d21f1372_files:/galaxy/server/database/objects/7/5/e/dataset_75e6bc1e-c1cd-4f26-a0a0-7653d21f1372.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:16,329 [pN:job_handler_0,p:9,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.handler DEBUG 2024-09-12 13:17:17,167 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 164 +tpv.core.entities DEBUG 2024-09-12 13:17:17,207 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:17:17,208 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (164) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:17:17,213 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (164) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:17:17,231 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (164) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:17:17,255 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (164) Working directory for job is: /galaxy/server/database/jobs_directory/000/164 +galaxy.jobs.runners DEBUG 2024-09-12 13:17:17,263 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [164] queued (50.151 ms) +galaxy.jobs.handler INFO 2024-09-12 13:17:17,271 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (164) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:17,276 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 164 +galaxy.jobs DEBUG 2024-09-12 13:17:17,399 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [164] prepared (98.228 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:17:17,421 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/164/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/164/registry.xml' '/galaxy/server/database/jobs_directory/000/164/upload_params.json' '194:/galaxy/server/database/objects/7/7/0/dataset_770714e4-2cfe-4e99-ab4d-71a3e1cd3534_files:/galaxy/server/database/objects/7/7/0/dataset_770714e4-2cfe-4e99-ab4d-71a3e1cd3534.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:17,435 [pN:job_handler_0,p:9,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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:17:21,896 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 162 finished +galaxy.model.metadata DEBUG 2024-09-12 13:17:21,957 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 192 +galaxy.jobs INFO 2024-09-12 13:17:21,998 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 162 in /galaxy/server/database/jobs_directory/000/162 +galaxy.jobs DEBUG 2024-09-12 13:17:22,056 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 162 executed (132.356 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:17:26,063 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 163: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:17:28,129 [pN:job_handler_0,p:9,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 2024-09-12 13:17:32,618 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 163 finished +galaxy.model.metadata DEBUG 2024-09-12 13:17:32,686 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 193 +galaxy.jobs INFO 2024-09-12 13:17:32,734 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 163 in /galaxy/server/database/jobs_directory/000/163 +galaxy.jobs DEBUG 2024-09-12 13:17:32,787 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 163 executed (138.356 ms) +galaxy.jobs.runners DEBUG 2024-09-12 13:17:34,482 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 164 finished +galaxy.model.metadata DEBUG 2024-09-12 13:17:34,546 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 194 +galaxy.jobs INFO 2024-09-12 13:17:34,632 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 164 in /galaxy/server/database/jobs_directory/000/164 +galaxy.jobs DEBUG 2024-09-12 13:17:34,688 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 164 executed (177.884 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:17:35,809 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 165 +tpv.core.entities DEBUG 2024-09-12 13:17:35,861 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:17:35,862 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (165) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:17:35,869 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (165) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:17:35,887 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (165) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:17:35,907 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (165) Working directory for job is: /galaxy/server/database/jobs_directory/000/165 +galaxy.jobs.runners DEBUG 2024-09-12 13:17:35,917 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [165] queued (47.823 ms) +galaxy.jobs.handler INFO 2024-09-12 13:17:35,922 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (165) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:35,926 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 165 +galaxy.jobs DEBUG 2024-09-12 13:17:36,089 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [165] prepared (140.375 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:36,089 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:17:36,090 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:36,284 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:17:36,309 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/165/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/165/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277_files && cp /galaxy/server/database/jobs_directory/000/165/configs/tmpfdzwd50p /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277_files /galaxy/server/database/jobs_directory/000/165/configs/tmpfdzwd50p && cp /galaxy/server/database/jobs_directory/000/165/configs/tmpexgo1yvs /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277.dat; cp /galaxy/server/database/jobs_directory/000/165/configs/tmpfdzwd50p /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:36,323 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] (165) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:36,336 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:17:36,336 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:36,358 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:42,282 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 165: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:17:48,619 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 165 finished +galaxy.model.metadata DEBUG 2024-09-12 13:17:48,715 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 195 +galaxy.util WARNING 2024-09-12 13:17:48,727 [pN:job_handler_0,p:9,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/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277.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/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277.dat' +galaxy.jobs INFO 2024-09-12 13:17:48,762 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 165 in /galaxy/server/database/jobs_directory/000/165 +galaxy.objectstore CRITICAL 2024-09-12 13:17:48,805 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpfdzwd50p' +galaxy.jobs DEBUG 2024-09-12 13:17:48,806 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 165 executed (154.002 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:17:50,287 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 166 +tpv.core.entities DEBUG 2024-09-12 13:17:50,328 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:17:50,328 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (166) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:17:50,334 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (166) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:17:50,353 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (166) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:17:50,374 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (166) Working directory for job is: /galaxy/server/database/jobs_directory/000/166 +galaxy.jobs.runners DEBUG 2024-09-12 13:17:50,383 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [166] queued (48.362 ms) +galaxy.jobs.handler INFO 2024-09-12 13:17:50,389 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (166) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:17:50,391 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 166 +galaxy.jobs DEBUG 2024-09-12 13:17:50,486 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [166] prepared (73.466 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:50,487 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:17:50,487 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:50,513 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:17:50,537 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/166/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/166/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e_files && cp /galaxy/server/database/jobs_directory/000/166/configs/tmptmt_gbdz /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e_files /galaxy/server/database/jobs_directory/000/166/configs/tmptmt_gbdz && cp /galaxy/server/database/jobs_directory/000/166/configs/tmp1mjmpwca /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e.dat; cp /galaxy/server/database/jobs_directory/000/166/configs/tmptmt_gbdz /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:17:50,552 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] (166) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:50,563 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:17:50,563 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:17:50,584 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-12 13:18:59,698 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 166: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:19:05,900 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 166 finished +galaxy.model.metadata DEBUG 2024-09-12 13:19:10,421 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 196 +galaxy.util WARNING 2024-09-12 13:19:11,342 [pN:job_handler_0,p:9,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/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e.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/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e.dat' +galaxy.jobs INFO 2024-09-12 13:19:11,377 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 166 in /galaxy/server/database/jobs_directory/000/166 +galaxy.objectstore CRITICAL 2024-09-12 13:19:11,424 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmp1mjmpwca' +galaxy.jobs DEBUG 2024-09-12 13:19:11,424 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 166 executed (5493.479 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:19:12,510 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 167 +tpv.core.entities DEBUG 2024-09-12 13:19:12,551 [pN:job_handler_0,p:9,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={'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=None, 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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:19:12,552 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (167) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:19:12,557 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (167) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:19:12,576 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (167) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:19:12,597 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (167) Working directory for job is: /galaxy/server/database/jobs_directory/000/167 +galaxy.jobs.runners DEBUG 2024-09-12 13:19:12,604 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [167] queued (46.750 ms) +galaxy.jobs.handler INFO 2024-09-12 13:19:12,608 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (167) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:19:12,613 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 167 +galaxy.jobs DEBUG 2024-09-12 13:19:12,729 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [167] prepared (96.909 ms) +galaxy.jobs.command_factory INFO 2024-09-12 13:19:12,751 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] 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' '197:/galaxy/server/database/objects/2/e/d/dataset_2ed33cef-cd23-4e80-84be-8480e7ce1da5_files:/galaxy/server/database/objects/2/e/d/dataset_2ed33cef-cd23-4e80-84be-8480e7ce1da5.dat'] +galaxy.jobs.runners DEBUG 2024-09-12 13:19:12,765 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-12 13:19:21,937 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 167: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-12 13:19:28,067 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 167 finished +galaxy.model.metadata DEBUG 2024-09-12 13:19:28,133 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 197 +galaxy.jobs INFO 2024-09-12 13:19:28,174 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 167 in /galaxy/server/database/jobs_directory/000/167 +galaxy.jobs DEBUG 2024-09-12 13:19:28,225 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 167 executed (128.487 ms) +galaxy.jobs.handler DEBUG 2024-09-12 13:19:29,015 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 168 +tpv.core.entities DEBUG 2024-09-12 13:19:29,060 [pN:job_handler_0,p:9,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={'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/jbrowse/jbrowse/.*, abstract=False, cores=1, mem=11.4, gpus=None, 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:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-12 13:19:29,060 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (168) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-12 13:19:29,066 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (168) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-12 13:19:29,084 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (168) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-12 13:19:29,103 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (168) Working directory for job is: /galaxy/server/database/jobs_directory/000/168 +galaxy.jobs.runners DEBUG 2024-09-12 13:19:29,113 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] Job [168] queued (46.172 ms) +galaxy.jobs.handler INFO 2024-09-12 13:19:29,117 [pN:job_handler_0,p:9,tN:JobHandlerQueue.monitor_thread] (168) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:19:29,122 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 168 +galaxy.jobs DEBUG 2024-09-12 13:19:29,234 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [168] prepared (90.872 ms) +galaxy.tool_util.deps.containers INFO 2024-09-12 13:19:29,235 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:19:29,236 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:19:29,259 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-12 13:19:29,282 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/168/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --version > /galaxy/server/database/jobs_directory/000/168/outputs/COMMAND_VERSION 2>&1; +mkdir -p /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files && cp /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 && cp /galaxy/server/database/jobs_directory/000/168/configs/tmpe_v1eztl /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat; cp /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat] +galaxy.jobs.runners DEBUG 2024-09-12 13:19:29,297 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (168) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-12 13:19:29,309 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-12 13:19:29,309 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1: mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428 +galaxy.tool_util.deps.containers INFO 2024-09-12 13:19:29,329 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-de19c44eeee083c68bc61ea8799d8cb400736db6:3adfd175d9eea4d6e2e69a89436cae9cba840428-0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-09-12 13:19:34,102 [pN:job_handler_0,p:9,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/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://10.16.0.1:443/apis/batch/v1/namespaces/prod-24-09-12-12-33-1/jobs/gxy-4grm7 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/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-4grm7": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-12 13:19:34,194 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] (168/gxy-4grm7) Terminated at user's request +galaxy.util WARNING 2024-09-12 13:19:34,279 [pN:job_handler_0,p:9,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/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.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/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat' +galaxy.objectstore CRITICAL 2024-09-12 13:19:34,304 [pN:job_handler_0,p:9,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmpe_v1eztl' diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/jobs.txt b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/jobs.txt new file mode 100644 index 000000000..5db3857ff --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/jobs.txt @@ -0,0 +1,168 @@ +c18cd423ba921e33 error 2024-09-12T13:19:34.271477 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +dc7c09f27f40b9bf ok 2024-09-12T13:19:28.178102 upload1 +699e2082416ee2d7 ok 2024-09-12T13:19:11.381884 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +86bca9ae0d4021b1 ok 2024-09-12T13:17:48.766824 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +265729caa41a1863 ok 2024-09-12T13:17:34.636641 upload1 +57899371865de695 ok 2024-09-12T13:17:32.738459 upload1 +f883ecbb9b4f587d ok 2024-09-12T13:17:22.003048 upload1 +051dc5929d40d789 error 2024-09-12T13:17:15.315642 upload1 +a532d0d970ae9556 ok 2024-09-12T13:17:04.362101 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +400c328259657a59 ok 2024-09-12T13:16:51.830736 upload1 +625eb35b22060e38 ok 2024-09-12T13:16:51.743709 upload1 +4fc6e5e22549ed60 ok 2024-09-12T13:16:32.791982 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +aad2d829deed67c5 ok 2024-09-12T13:16:17.071161 upload1 +44efe9bb9ae12026 ok 2024-09-12T13:16:17.039156 upload1 +b2a75b95a3a0943f ok 2024-09-12T13:15:57.186601 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +ff7864dc2243e76c ok 2024-09-12T13:15:41.154580 upload1 +a32388ba8406a825 ok 2024-09-12T13:15:40.991889 upload1 +8fb27de822c69f14 ok 2024-09-12T13:15:40.977599 upload1 +4b01e22ab2d6bf1d ok 2024-09-12T13:15:38.172968 upload1 +2dffea7156c2f946 ok 2024-09-12T13:15:27.893700 upload1 +4d3917006796995f ok 2024-09-12T13:15:27.887340 upload1 +ce4af30f258cf54a ok 2024-09-12T13:15:27.804869 upload1 +9829468d3ed3fcc2 ok 2024-09-12T13:15:23.502174 upload1 +2bca21c51737a187 ok 2024-09-12T13:15:10.277573 upload1 +be30d4637f5963c9 ok 2024-09-12T13:15:09.203474 upload1 +e6d2b9fbd0c20be3 error 2024-09-12T13:14:59.814455 upload1 +3cc54e8bef500661 ok 2024-09-12T13:14:48.598319 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +3182a5404b7e43fc ok 2024-09-12T13:14:35.488464 upload1 +2ba83b5637b11a77 ok 2024-09-12T13:14:16.161470 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +11d465ee0edd0d83 ok 2024-09-12T13:13:40.701746 upload1 +4233d6fecc29bcb4 ok 2024-09-12T13:13:21.472341 toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0 +e130bbdb3c861c75 ok 2024-09-12T13:13:05.327085 upload1 +12a3dc4644eabc47 ok 2024-09-12T13:13:05.092428 upload1 +24cfce1dc6c71df2 ok 2024-09-12T13:13:05.052178 upload1 +98e036e4ea2088a4 ok 2024-09-12T13:12:41.519949 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +50a2fd9b130b93e8 ok 2024-09-12T13:12:25.209882 upload1 +2bd05dec28ce1858 ok 2024-09-12T13:12:24.046160 upload1 +c33fcc83aebe3540 ok 2024-09-12T13:12:06.623955 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +91d1501bd87ed579 ok 2024-09-12T13:11:51.761984 upload1 +3e95a027352f28e3 ok 2024-09-12T13:11:50.757928 upload1 +1381c17b42c4ef57 ok 2024-09-12T13:11:32.590636 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +2ab81e2d4b71799c ok 2024-09-12T13:11:18.744396 upload1 +c2f7be24d9d7ec02 ok 2024-09-12T13:11:17.854786 upload1 +41b4826423ace419 ok 2024-09-12T13:11:17.809564 upload1 +e6356d72fa49a643 ok 2024-09-12T13:10:56.705976 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +7e6953ebfeef6cf5 ok 2024-09-12T13:10:42.698036 upload1 +fd08b9561a6a74c9 ok 2024-09-12T13:10:42.690868 upload1 +ac547a96e883f049 ok 2024-09-12T13:10:23.818336 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +723cd653c4003079 ok 2024-09-12T13:10:04.172035 upload1 +4d8affd50551d18d ok 2024-09-12T13:10:04.112249 upload1 +b034089172991e96 ok 2024-09-12T13:09:43.176456 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0 +20648ae42cde3ac9 ok 2024-09-12T13:09:03.626110 upload1 +2674611b25736722 ok 2024-09-12T13:09:02.624250 upload1 +238c44441d96e1db ok 2024-09-12T13:08:43.339116 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0 +ce1f06ce12851c2c ok 2024-09-12T13:08:04.844279 upload1 +2c14ff1b8ee62486 ok 2024-09-12T13:07:45.368130 toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0 +fce5b510e68a9618 ok 2024-09-12T13:07:08.294750 upload1 +f981cf37215e9a69 error 2024-09-12T13:06:49.067855 upload1 +77906ef2693d8471 error 2024-09-12T13:06:36.861985 toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0 +85cb168af7ca14a8 ok 2024-09-12T13:06:24.867543 upload1 +9525a30c8a9072dd ok 2024-09-12T13:06:23.852091 upload1 +ff6e2b9c7b9ced76 ok 2024-09-12T13:06:06.085492 toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0 +e6fd73ebb5425103 ok 2024-09-12T13:05:43.353588 upload1 +5bc6dfeed7ce6fa3 ok 2024-09-12T13:05:22.836130 toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0 +1187daf3bc7c494c ok 2024-09-12T13:04:22.720171 upload1 +63d91ea30daf1b8b ok 2024-09-12T13:04:02.449599 toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0 +cc6bbb75288650e0 ok 2024-09-12T13:03:42.989692 upload1 +83e05db61a08dd9c ok 2024-09-12T13:03:31.804838 upload1 +740b63cd736b2680 error 2024-09-12T13:03:24.964889 upload1 +0dcb287ce11a5b32 ok 2024-09-12T13:03:12.732699 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4 +95852cd1d8428b7e ok 2024-09-12T13:03:00.183019 upload1 +41674f4dd3174743 ok 2024-09-12T13:03:00.148965 upload1 +3cad2cf35f5d9343 ok 2024-09-12T13:02:42.017728 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4 +f539267d09cbfe36 ok 2024-09-12T13:02:28.113413 upload1 +fd2eba97839297b7 ok 2024-09-12T13:02:27.123442 upload1 +d4b33cdaafb9bfa2 ok 2024-09-12T13:02:07.798512 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4 +25aeaab9487541dc ok 2024-09-12T13:01:49.653750 upload1 +b5427a5b0184928f ok 2024-09-12T13:01:30.539803 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +fde3b789746cd95e ok 2024-09-12T13:01:17.792142 upload1 +be1f2aed24ce2f5c ok 2024-09-12T13:01:16.767966 upload1 +469cdd2cf6d960e5 ok 2024-09-12T13:00:57.852443 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +91a1955d508039b8 ok 2024-09-12T13:00:44.739088 upload1 +5df38637de07fb27 ok 2024-09-12T13:00:43.789720 upload1 +03e219fa5fcd79bd ok 2024-09-12T13:00:24.739464 upload1 +bde1698b9e2a4825 error 2024-09-12T13:00:17.182571 upload1 +38c09c9a2bc29dd8 ok 2024-09-12T13:00:05.507129 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +eee888d0b36cb2fd ok 2024-09-12T12:59:53.222068 upload1 +27f2648071450994 ok 2024-09-12T12:59:53.197472 upload1 +6b51ea164066a648 ok 2024-09-12T12:59:34.448249 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +11e89e0c17d36cde ok 2024-09-12T12:59:21.114725 upload1 +96bac482d8b094fa ok 2024-09-12T12:59:20.039939 upload1 +2e58c3969419a55a ok 2024-09-12T12:59:01.998278 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +c5cabb4145f8077b ok 2024-09-12T12:58:47.178442 upload1 +63bddd09d6f30036 ok 2024-09-12T12:58:47.108966 upload1 +6eeb166682ad9739 ok 2024-09-12T12:58:47.083867 upload1 +68fd8f700c6e614d ok 2024-09-12T12:58:47.039526 upload1 +812c73de05e41966 ok 2024-09-12T12:58:18.057286 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +3d3f85972e8b91fb ok 2024-09-12T12:58:05.581793 upload1 +e463b4b86f134ffb ok 2024-09-12T12:57:45.515258 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +ba9f1a22493fe972 ok 2024-09-12T12:57:33.001895 upload1 +74f3069d5b02ebba ok 2024-09-12T12:57:12.960692 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +8d0368a457c88265 ok 2024-09-12T12:56:56.732536 upload1 +02250aa4de4cbc16 ok 2024-09-12T12:56:37.204617 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +edc9d596a056686d ok 2024-09-12T12:56:20.152694 upload1 +7b5b892ecab82f4f ok 2024-09-12T12:56:01.904049 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +375f09a9538356a1 ok 2024-09-12T12:55:37.718093 upload1 +ecc08807fdb2a45f ok 2024-09-12T12:55:36.843283 upload1 +779365dce838fb80 ok 2024-09-12T12:55:18.008149 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +fa3eb0e5a4186459 ok 2024-09-12T12:54:57.088771 upload1 +ea65639b0567a69e ok 2024-09-12T12:54:51.090223 upload1 +efeda1d9cad1b77b ok 2024-09-12T12:54:50.529311 upload1 +c73db28eb5910f24 ok 2024-09-12T12:54:50.463999 upload1 +95927bf4fee2d0d0 ok 2024-09-12T12:54:50.170692 upload1 +7117a621f666bab2 error 2024-09-12T12:54:37.187822 upload1 +f59e9accad7eabd6 ok 2024-09-12T12:54:36.766509 upload1 +ac951076f76db0d2 ok 2024-09-12T12:54:36.638683 upload1 +d6038aebc5a208f9 ok 2024-09-12T12:54:36.617345 upload1 +61b2ac79367bf1c8 ok 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a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/node-info.txt b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/node-info.txt new file mode 100644 index 000000000..c1bdc97d5 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/node-info.txt @@ -0,0 +1,146 @@ +Name: gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv +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-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-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv + 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: 1904756533591236315 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv","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: Thu, 12 Sep 2024 12:40:27 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv + AcquireTime: + RenewTime: Thu, 12 Sep 2024 13:20:13 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + CorruptDockerOverlay2 False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + FrequentKubeletRestart False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 NoFrequentKubeletRestart kubelet is functioning properly + DeprecatedPullingSchemaV1Image False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 DeprecatedPullingSchemaV1ImageDetected No deprecation risk: did not pull any schema v1 images + FrequentUnregisterNetDevice False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 NoFrequentUnregisterNetDevice node is functioning properly + DeprecatedAuthsFieldInContainerdConfiguration False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 DeprecatedAuthsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'auths' field in containerd's config + DeprecatedUsingV1Alpha2Cri False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 DeprecatedUsingV1Alpha2CriNotDetected No deprecation risk: did not use v1alpha2 CRI + SysctlChanged False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 SysctlNotChanged Default sysctls are in effect, no unexpected sysctl changes + DeprecatedConfigsFieldInContainerdConfiguration False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 DeprecatedConfigsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'configs' field in containerd's config + FrequentContainerdRestart False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 NoFrequentContainerdRestart containerd is functioning properly + KernelDeadlock False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 KernelHasNoDeadlock kernel has no deadlock + DeprecatedOtherContainerdFeatures False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +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. + FrequentDockerRestart False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 NoFrequentDockerRestart docker is functioning properly + ReadonlyFilesystem False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + DeprecatedMirrorsFieldInContainerdConfiguration False Thu, 12 Sep 2024 13:15:33 +0000 Thu, 12 Sep 2024 12:40:27 +0000 DeprecatedMirrorsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'mirrors' field in containerd's config + NetworkUnavailable False Thu, 12 Sep 2024 12:40:28 +0000 Thu, 12 Sep 2024 12:40:27 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Thu, 12 Sep 2024 13:19:23 +0000 Thu, 12 Sep 2024 12:40:17 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Thu, 12 Sep 2024 13:19:23 +0000 Thu, 12 Sep 2024 12:40:17 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Thu, 12 Sep 2024 13:19:23 +0000 Thu, 12 Sep 2024 12:40:17 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Thu, 12 Sep 2024 13:19:23 +0000 Thu, 12 Sep 2024 12:40:48 +0000 KubeletReady kubelet is posting ready status. AppArmor enabled +Addresses: + InternalIP: 10.142.15.218 + ExternalIP: 34.138.42.75 + Hostname: gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv +Capacity: + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82369080Ki + pods: 110 +Allocatable: + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75554360Ki + pods: 110 +System Info: + Machine ID: 55c884808e587c8e97356498e126734e + System UUID: 55c88480-8e58-7c8e-9735-6498e126734e + Boot ID: 16afe659-8d59-4d36-b2a8-0c0114a33aa4 + Kernel Version: 6.1.85+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.7.15 + Kubelet Version: v1.28.12-gke.1052000 + Kube-Proxy Version: v1.28.12-gke.1052000 +PodCIDR: 10.0.0.0/24 +PodCIDRs: 10.0.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv +Non-terminated Pods: (26 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + gmp-system collector-zph8l 5m (0%) 0 (0%) 36M (0%) 3032M (3%) 39m + gmp-system gmp-operator-69476d8768-f9w5n 1m (0%) 0 (0%) 16M (0%) 2G (2%) 40m + kube-system event-exporter-gke-58c99c7869-2ttl4 3m (0%) 0 (0%) 100Mi (0%) 0 (0%) 40m + kube-system fluentbit-gke-qtbb5 100m (0%) 0 (0%) 200Mi (0%) 500Mi (0%) 39m + kube-system gke-metrics-agent-88xvp 9m (0%) 0 (0%) 110Mi (0%) 110Mi (0%) 39m + kube-system konnectivity-agent-6589cc9484-qrgph 15m (0%) 0 (0%) 60Mi (0%) 155Mi (0%) 40m + kube-system konnectivity-agent-autoscaler-697695f8c5-mjx9d 10m (0%) 0 (0%) 10M (0%) 0 (0%) 40m + kube-system kube-dns-6f955b858b-gx9lk 260m (1%) 0 (0%) 110Mi (0%) 210Mi (0%) 40m + kube-system kube-dns-autoscaler-755c7dfdf5-6mf7t 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 40m + kube-system kube-proxy-gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv 100m (0%) 0 (0%) 0 (0%) 0 (0%) 38m + kube-system l7-default-backend-85b45d5c78-jmhps 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 40m + kube-system metrics-server-v0.7.0-7787fd6556-92lpm 48m (0%) 43m (0%) 105Mi (0%) 355Mi (0%) 39m + kube-system pdcsi-node-jm5wj 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 39m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-cvmfscsi-controllerplugin-585456b67c4qt64 0 (0%) 0 (0%) 0 (0%) 0 (0%) 37m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-cvmfscsi-nodeplugin-rmq7t 0 (0%) 0 (0%) 0 (0%) 0 (0%) 32m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-celery-6dbfb4575d-pbvlp 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-celery-beat-5998d97fbf-zjr5m 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-job-0-77859d4b7c-sd2hk 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-nginx-7dff99c8bc-cnq4n 100m (0%) 2 (10%) 500M (0%) 3G (3%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-web-7b45c47477-2vjwj 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-galaxy-workflow-77f8fff9-lrmbn 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 37m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-rabbitmq-98bb869f6-94g8x 0 (0%) 0 (0%) 0 (0%) 0 (0%) 37m + prod-24-09-12-12-33-1 prod-24-09-12-12-33-1-rabbitmq-messaging-topology-operators79pt 0 (0%) 0 (0%) 0 (0%) 0 (0%) 37m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4441m (22%) 14043m (70%) + memory 13748622464 (17%) 51678947328 (66%) + ephemeral-storage 35Gi (79%) 200Gi (456%) + hugepages-1Gi 0 (0%) 0 (0%) + hugepages-2Mi 0 (0%) 0 (0%) +Events: + Type Reason Age From Message + ---- ------ ---- ---- ------- + Normal Starting 39m kube-proxy + Normal Starting 43m kubelet Starting kubelet. + Warning InvalidDiskCapacity 43m kubelet invalid capacity 0 on image filesystem + Normal NodeAllocatableEnforced 43m kubelet Updated Node Allocatable limit across pods + Normal NodeHasNoDiskPressure 41m (x7 over 43m) kubelet Node gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 41m (x7 over 43m) kubelet Node gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 41m (x8 over 43m) kubelet Node gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv status is now: NodeHasSufficientMemory + Warning NodeRegistrationCheckerStart 39m node-registration-checker-monitor Thu Sep 12 12:36:36 UTC 2024 - ** Starting Node Registration Checker ** + Normal Synced 39m cloud-node-controller Node synced successfully + Normal RegisteredNode 39m node-controller Node gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv event: Registered Node gke-prod-24-09-12-12-33-default-pool-b0a3710b-zdlv in Controller + Warning NodeRegistrationCheckerDidNotRunChecks 36m node-registration-checker-monitor Thu Sep 12 12:43:37 UTC 2024 - ** Node ready and registered. ** diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.html b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.html new file mode 100644 index 000000000..a9279b77a --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
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+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.json b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.json new file mode 100644 index 000000000..62dc21352 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-12-12-33-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 57, "errors": 21, "failures": 4, "skips": 0}, "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": 33.40319490432739, "inputs": {"input_files": [{"src": "hda", "id": "20648ae42cde3ac9"}, {"src": "hda", "id": "2674611b25736722"}], "sec_default|nfiles": "=2", "output_type": "v"}, "job": {"model_class": "Job", "id": "3cad2cf35f5d9343", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:02:42.017728", "create_time": "2024-09-12T13:02:28.406367", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4", "history_id": "45fb41c325e9adff", "external_id": "gxy-cvl4f", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/6/1/dataset_361253bb-25bf-4a64-95a1-a475f3db7433.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/8/a/c/dataset_8acfbc0d-5b45-44a7-985b-2ad58066876e.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools isec --nfiles \"=2\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/0/7/5/dataset_075f3793-0e1a-4beb-94ca-bb36a9981d6e.dat'", "traceback": null, "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\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_files": {"id": "20648ae42cde3ac9", "src": "hda", "uuid": "361253bb-25bf-4a64-95a1-a475f3db7433"}, "input_files1": {"id": "20648ae42cde3ac9", "src": "hda", "uuid": "361253bb-25bf-4a64-95a1-a475f3db7433"}, "input_files2": {"id": "2674611b25736722", "src": "hda", "uuid": "8acfbc0d-5b45-44a7-985b-2ad58066876e"}}, "outputs": {"output_file": {"id": "b034089172991e96", "src": "hda", "uuid": "075f3793-0e1a-4beb-94ca-bb36a9981d6e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: -w option not given, printing list of sites...\n", "job_stdout": "", "job_stderr": "", "stderr": "Note: -w option not given, printing list of sites...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:02:31", "plugin": "core", "name": "end_epoch", "raw_value": "1726146151.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:02:30", "plugin": "core", "name": "start_epoch", "raw_value": "1726146150.0000000"}, {"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_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": 30.785812377929688, "inputs": {"input_files": [{"src": "hda", "id": "723cd653c4003079"}, {"src": "hda", "id": "4d8affd50551d18d"}], "sec_restrict|regions_overlap": "1", "sec_default|nfiles": "=2", "output_type": "v"}, "job": {"model_class": "Job", "id": "0dcb287ce11a5b32", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:03:12.732699", "create_time": "2024-09-12T13:03:00.494273", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.15.1+galaxy4", "history_id": "45fb41c325e9adff", "external_id": "gxy-lqmd5", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/4/3/dataset_143ea450-55ff-4c22-956e-9d122de8fa19.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/0/d/6/dataset_0d65ace0-2d11-4ff5-a0b9-d676dfad5c01.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/6/4/0/dataset_64086215-a423-4ef4-a4f6-1e3f581b1a51.dat'", "traceback": null, "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": "723cd653c4003079", "src": "hda", "uuid": "143ea450-55ff-4c22-956e-9d122de8fa19"}, "input_files1": {"id": "723cd653c4003079", "src": "hda", "uuid": "143ea450-55ff-4c22-956e-9d122de8fa19"}, "input_files2": {"id": "4d8affd50551d18d", "src": "hda", "uuid": "0d65ace0-2d11-4ff5-a0b9-d676dfad5c01"}}, "outputs": {"output_file": {"id": "ac547a96e883f049", "src": "hda", "uuid": "64086215-a423-4ef4-a4f6-1e3f581b1a51"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: -w option not given, printing list of sites...\n", "job_stdout": "", "job_stderr": "", "stderr": "Note: -w option not given, printing list of sites...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:03:03", "plugin": "core", "name": "end_epoch", "raw_value": "1726146183.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:03:02", "plugin": "core", "name": "start_epoch", "raw_value": "1726146182.0000000"}, {"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": 35.966850996017456, "inputs": {"input_file": {"src": "hda", "id": "ce1f06ce12851c2c"}}, "job": {"model_class": "Job", "id": "d4b33cdaafb9bfa2", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:02:07.798512", "create_time": "2024-09-12T13:01:50.088423", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.15.1+galaxy4", "history_id": "45fb41c325e9adff", "external_id": "gxy-97b4n", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/0/3/dataset_c034a870-49be-45c0-8d6f-41bfb69ca909.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools query --list-samples input.vcf.gz | tee /galaxy/server/database/objects/f/6/f/dataset_f6f7a9f1-cf41-4282-8ed4-ad82b68c6bfb.dat | tr '\\n' ','", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_file": {"id": "ce1f06ce12851c2c", "src": "hda", "uuid": "c034a870-49be-45c0-8d6f-41bfb69ca909"}}, "outputs": {"output_file": {"id": "238c44441d96e1db", "src": "hda", "uuid": "f6f7a9f1-cf41-4282-8ed4-ad82b68c6bfb"}}, "output_collections": {}, "tool_stdout": "C,D,", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "C,D,", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-12 13:01:56", "plugin": "core", "name": "end_epoch", "raw_value": "1726146116.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:01:56", "plugin": "core", "name": "start_epoch", "raw_value": "1726146116.0000000"}, {"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": "column_remove_by_header/1.0-0", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "1.0", "test_index": 0, "time_seconds": 40.69732475280762, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "column_remove_by_header/1.0-1", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "1.0", "test_index": 1, "time_seconds": 59.12560033798218, "inputs": {"input_tabular": {"src": "hda", "id": "d51e0424dc6ec33a"}, "headers_0|name": "KEY", "headers_1|name": "a", "keep_columns": true, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "2b9702019bfaa3f8", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T12:51:20.697270", "create_time": "2024-09-12T12:50:38.948946", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0", "history_id": "45fb41c325e9adff", "external_id": "gxy-qkf7w", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/2040e4c2750a/column_remove_by_header/column_remove_by_header.py' -i '/galaxy/server/database/objects/9/c/2/dataset_9c24e152-6edd-41bd-9bce-ab69133f9801.dat' -o '/galaxy/server/database/objects/4/5/7/dataset_45747e63-703c-4d81-af9d-856d8f1ea040.dat' -d '\t' --keep -s '#' --unicode-escaped-cols --columns 'KEY' 'a'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strip_characters": "\"#\"", "keep_columns": "true", "headers": "[{\"__index__\": 0, \"name\": \"KEY\"}, {\"__index__\": 1, \"name\": \"a\"}]"}, "inputs": {"input_tabular": {"id": "d51e0424dc6ec33a", "src": "hda", "uuid": "9c24e152-6edd-41bd-9bce-ab69133f9801"}}, "outputs": {"output_tabular": {"id": "2b9702019bfaa3f8", "src": "hda", "uuid": "45747e63-703c-4d81-af9d-856d8f1ea040"}}, "output_collections": {}, "tool_stdout": "Kept 2 of 5 columns.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Kept 2 of 5 columns.\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 12:51:10", "plugin": "core", "name": "end_epoch", "raw_value": "1726145470.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 12:51:09", "plugin": "core", "name": "start_epoch", "raw_value": "1726145469.0000000"}, {"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": "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": 57.30671143531799, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "3cc54e8bef500661"}, {"src": "hda", "id": "3cc54e8bef500661"}], "advancedOpt|showAdvancedOpt": "no", "output|showOutputSettings": "no"}, "job": {"model_class": "Job", "id": "238c44441d96e1db", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:08:43.339116", "create_time": "2024-09-12T13:08:05.265458", "galaxy_version": "23.1", "command_version": "plotFingerprint 3.5.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", "history_id": "45fb41c325e9adff", "external_id": "gxy-jwt8m", "command_line": "ln -s '/galaxy/server/database/objects/d/0/b/dataset_d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/1/metadata_8014a213-3e17-4886-a8bc-1311216ae213.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/d/0/b/dataset_d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/1/metadata_8014a213-3e17-4886-a8bc-1311216ae213.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/e/7/8/dataset_e7828476-49b3-49f3-9f48-e3757769d5f5.dat --plotFileFormat 'png'", "traceback": 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\": 142, \"src\": \"hda\"}, {\"id\": 142, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibam_conditional|bamfiles": {"id": "3cc54e8bef500661", "src": "hda", "uuid": "d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea"}, "multibam_conditional|bamfiles1": {"id": "3cc54e8bef500661", "src": "hda", "uuid": "d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea"}, "multibam_conditional|bamfiles2": {"id": "3cc54e8bef500661", "src": "hda", "uuid": "d0bc1a9e-a42f-4b0b-8c31-c6543ec85fea"}}, "outputs": {"outFileName": {"id": "e6d2b9fbd0c20be3", "src": "hda", "uuid": "e7828476-49b3-49f3-9f48-e3757769d5f5"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "10 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "10.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:08:30", "plugin": "core", "name": "end_epoch", "raw_value": "1726146510.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:08:20", "plugin": "core", "name": "start_epoch", "raw_value": "1726146500.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_plot_fingerprint/3.5.4+galaxy0-1", "has_data": true, "data": {"tool_id": "deeptools_plot_fingerprint", "tool_version": "3.5.4+galaxy0", "test_index": 1, "time_seconds": 60.66046118736267, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "2bca21c51737a187"}, {"src": "hda", "id": "2bca21c51737a187"}], "advancedOpt|plotTitle": "Test Fingerprint Plot", "advancedOpt|showAdvancedOpt": "yes", "output|saveRawCounts": true, "output|saveQualityMetrics": true, "output|JSDsample": {"src": "hda", "id": "2bca21c51737a187"}, "output|showOutputSettings": "yes"}, "job": {"model_class": "Job", "id": "b034089172991e96", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:09:43.176456", "create_time": "2024-09-12T13:09:04.116118", "galaxy_version": "23.1", "command_version": "plotFingerprint 3.5.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", "history_id": "45fb41c325e9adff", "external_id": "gxy-x8bx9", "command_line": "ln -s '/galaxy/server/database/objects/3/e/3/dataset_3e32ed29-1dc8-4673-a182-bafe2b392107.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/3/2/5/metadata_3250c116-496e-4577-8a75-c473e8459824.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/3/e/3/dataset_3e32ed29-1dc8-4673-a182-bafe2b392107.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/3/2/5/metadata_3250c116-496e-4577-8a75-c473e8459824.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/5/1/8/dataset_51817478-8918-4804-9ab3-3083e76b6d49.dat --plotFileFormat png --outRawCounts '/galaxy/server/database/objects/e/2/2/dataset_e228c695-27f7-4b5b-aec9-d1a91098c61a.dat' --outQualityMetrics '/galaxy/server/database/objects/f/3/4/dataset_f34cd567-9074-4d84-abf5-4758373d9b9c.dat' --JSDsample '0.bam' --binSize '500' --numberOfSamples '100000' --plotTitle 'Test Fingerprint Plot' --minMappingQuality '1'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output": "{\"JSDsample\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"__current_case__\": 1, \"outFileFormat\": \"png\", \"saveQualityMetrics\": true, \"saveRawCounts\": true, \"showOutputSettings\": \"yes\"}", "advancedOpt": "{\"__current_case__\": 1, \"binSize\": \"500\", \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"ignoreDuplicates\": false, \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"numberOfSamples\": \"100000\", \"plotTitle\": \"Test Fingerprint Plot\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false}", "region": "\"\"", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}, {\"id\": 145, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibam_conditional|bamfiles": {"id": "2bca21c51737a187", "src": "hda", "uuid": "3e32ed29-1dc8-4673-a182-bafe2b392107"}, "multibam_conditional|bamfiles1": {"id": "2bca21c51737a187", "src": "hda", "uuid": "3e32ed29-1dc8-4673-a182-bafe2b392107"}, "multibam_conditional|bamfiles2": {"id": "2bca21c51737a187", "src": "hda", "uuid": "3e32ed29-1dc8-4673-a182-bafe2b392107"}, "output|JSDsample": {"id": "2bca21c51737a187", "src": "hda", "uuid": "3e32ed29-1dc8-4673-a182-bafe2b392107"}}, "outputs": {"outFileName": {"id": "9829468d3ed3fcc2", "src": "hda", "uuid": "51817478-8918-4804-9ab3-3083e76b6d49"}, "outFileRawCounts": {"id": "4d3917006796995f", "src": "hda", "uuid": "e228c695-27f7-4b5b-aec9-d1a91098c61a"}, "outFileQualityMetrics": {"id": "ce4af30f258cf54a", "src": "hda", "uuid": "f34cd567-9074-4d84-abf5-4758373d9b9c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "28 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "28.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:09:33", "plugin": "core", "name": "end_epoch", "raw_value": "1726146573.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:09:05", "plugin": "core", "name": "start_epoch", "raw_value": "1726146545.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "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": 39.15398168563843, "inputs": {"filtered_tsv": {"src": "hda", "id": "86bca9ae0d4021b1"}, "primers_bed": {"src": "hda", "id": "699e2082416ee2d7"}, "primers_tsv": {"src": "hda", "id": "dc7c09f27f40b9bf"}}, "job": {"model_class": "Job", "id": "4233d6fecc29bcb4", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:13:21.472341", "create_time": "2024-09-12T13:13:05.713750", "galaxy_version": "23.1", "command_version": "iVar version 1.2.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0", "history_id": "45fb41c325e9adff", "external_id": "gxy-hstxc", "command_line": "ivar getmasked -i '/galaxy/server/database/objects/2/0/3/dataset_2031316f-3985-4d58-8ecf-b985dcebff03.dat' -b '/galaxy/server/database/objects/a/8/d/dataset_a8d0bc7c-240a-48b0-ab29-652f0d7a6797.dat' -f '/galaxy/server/database/objects/8/a/8/dataset_8a8438d1-3af6-4f3f-8507-1e8f58316b06.dat' -p masked_primers", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"filtered_tsv": {"id": "86bca9ae0d4021b1", "src": "hda", "uuid": "2031316f-3985-4d58-8ecf-b985dcebff03"}, "primers_bed": {"id": "699e2082416ee2d7", "src": "hda", "uuid": "a8d0bc7c-240a-48b0-ab29-652f0d7a6797"}, "primers_tsv": {"id": "dc7c09f27f40b9bf", "src": "hda", "uuid": "8a8438d1-3af6-4f3f-8507-1e8f58316b06"}}, "outputs": {"masked": {"id": "c18cd423ba921e33", "src": "hda", "uuid": "49cf346a-e35d-4591-b87a-bcca8b09a449"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-12 13:13:11", "plugin": "core", "name": "end_epoch", "raw_value": "1726146791.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:13:11", "plugin": "core", "name": "start_epoch", "raw_value": "1726146791.0000000"}, {"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": "jbrowse/1.16.11+galaxy1-0", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 0, "time_seconds": 53.63866114616394, "inputs": {"reference_genome|genome": {"src": "hda", "id": "6a84b077126026d8"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "2ba83b5637b11a77", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:14:16.161470", "create_time": "2024-09-12T13:13:41.097456", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-nr2vs", "command_line": "mkdir -p /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36_files && cp /galaxy/server/database/jobs_directory/000/140/configs/tmp0zdx0ef8 /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36_files /galaxy/server/database/jobs_directory/000/140/configs/tmp0zdx0ef8 && cp /galaxy/server/database/jobs_directory/000/140/configs/tmp1mv6jzvr /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36.dat; cp /galaxy/server/database/jobs_directory/000/140/configs/tmp0zdx0ef8 /galaxy/server/database/objects/1/5/1/dataset_151af2fc-a849-4d81-a26f-d93fbbd38c36.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 169, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "6a84b077126026d8", "src": "hda", "uuid": "f2f6526b-1c0c-4b3b-96b2-2387f3fb4fe6"}}, "outputs": {"output": {"id": "99ee7488e8cde68a", "src": "hda", "uuid": "151af2fc-a849-4d81-a26f-d93fbbd38c36"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:14:01", "plugin": "core", "name": "end_epoch", "raw_value": "1726146841.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:14:00", "plugin": "core", "name": "start_epoch", "raw_value": "1726146840.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-1", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 1, "time_seconds": 32.219630002975464, "inputs": {"reference_genome|genome": {"src": "hda", "id": "83556fc4cfbbbc04"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "3cc54e8bef500661", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:14:48.598319", "create_time": "2024-09-12T13:14:35.643097", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-9fbkz", "command_line": "mkdir -p /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370_files && cp /galaxy/server/database/jobs_directory/000/142/configs/tmp8ze933lk /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370_files /galaxy/server/database/jobs_directory/000/142/configs/tmp8ze933lk && cp /galaxy/server/database/jobs_directory/000/142/configs/tmp0e8diaxb /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370.dat; cp /galaxy/server/database/jobs_directory/000/142/configs/tmp8ze933lk /galaxy/server/database/objects/5/6/9/dataset_569e7ab6-0941-49e3-9001-791335f57370.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 171, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "83556fc4cfbbbc04", "src": "hda", "uuid": "f4d527b9-8f60-4a69-a540-25737016bd88"}}, "outputs": {"output": {"id": "a990423c751ccda3", "src": "hda", "uuid": "569e7ab6-0941-49e3-9001-791335f57370"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:14:38", "plugin": "core", "name": "end_epoch", "raw_value": "1726146878.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:14:37", "plugin": "core", "name": "start_epoch", "raw_value": "1726146877.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-2", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 2, "time_seconds": 10.827890396118164, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "jbrowse/1.16.11+galaxy1-3", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 3, "time_seconds": 57.829920291900635, "inputs": {"reference_genome|genome": {"src": "hda", "id": "6c04daf964c3ff2e"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Auto Coloured", "track_groups_0|data_tracks_0|data_format|annotation": [{"src": "hda", "id": "157499d327befe1c"}, {"src": "hda", "id": "f1a9d9eba899dec5"}, {"src": "hda", "id": "6be692895ae06cac"}, {"src": "hda", "id": "33e24f900cb076cb"}], "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_1|category": "Ignore Scale", "track_groups_1|data_tracks_0|data_format|annotation": {"src": "hda", "id": "1705eea1fb43e55b"}, "track_groups_1|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|style_color": "#ff00ff", "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|color_select": "manual", "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_1|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_2|category": "Scaled Colour", "track_groups_2|data_tracks_0|data_format|annotation": {"src": "hda", "id": "1705eea1fb43e55b"}, "track_groups_2|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scales|scale_select": "automatic", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "automatic", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_1|data_format|annotation": {"src": "hda", "id": "1705eea1fb43e55b"}, "track_groups_2|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scales|scale_select": "automatic", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|style_color": "#0000ff", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "manual", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_1|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_2|data_format|annotation": {"src": "hda", "id": "1705eea1fb43e55b"}, "track_groups_2|data_tracks_2|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|minimum": "0", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|maximum": "1000", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|scale_select": "manual", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "automatic", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_2|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_3|data_format|annotation": {"src": "hda", "id": "1705eea1fb43e55b"}, "track_groups_2|data_tracks_3|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|minimum": "0", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|maximum": "1000", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|scale_select": "manual", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|style_color": "#ff0000", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "manual", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_3|data_format|data_format_select": "gene_calls", "track_groups_3|category": "Realistic", "track_groups_3|data_tracks_0|data_format|annotation": {"src": "hda", "id": "8bd04279d51376b3"}, "track_groups_3|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_3|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_3|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_3|data_tracks_1|data_format|annotation": {"src": "hda", "id": "047b421f54b03370"}, "track_groups_3|data_tracks_1|data_format|match_part|name": "cDNA_match", "track_groups_3|data_tracks_1|data_format|match_part|match_part_select": true, "track_groups_3|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_3|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "b2a75b95a3a0943f", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:15:57.186601", "create_time": "2024-09-12T13:15:41.582780", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-p4tzh", "command_line": "mkdir -p /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8_files && cp /galaxy/server/database/jobs_directory/000/154/configs/tmpl8s3cdk_ /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8_files /galaxy/server/database/jobs_directory/000/154/configs/tmpl8s3cdk_ && cp /galaxy/server/database/jobs_directory/000/154/configs/tmpv5z9yaqs /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8.dat; cp /galaxy/server/database/jobs_directory/000/154/configs/tmpl8s3cdk_ /galaxy/server/database/objects/d/9/4/dataset_d948342e-ce67-4433-80ef-7e1c33dcc6e8.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Auto Coloured\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 177, \"src\": \"hda\"}, {\"id\": 178, \"src\": \"hda\"}, {\"id\": 179, \"src\": \"hda\"}, {\"id\": 180, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Ignore Scale\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#ff00ff\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Scaled Colour\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 0, \"scale_select\": \"automatic\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#0000ff\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 0, \"scale_select\": \"automatic\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 1, \"maximum\": \"1000\", \"minimum\": \"0\", \"scale_select\": \"manual\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 3, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#ff0000\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 1, \"maximum\": \"1000\", \"minimum\": \"0\", \"scale_select\": \"manual\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 3, \"category\": \"Realistic\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 182, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 183, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 0, \"match_part_select\": true, \"name\": \"cDNA_match\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 176, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "6c04daf964c3ff2e", "src": "hda", "uuid": "d30b799e-3ce2-4da4-87c0-800c9ed1aea9"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "157499d327befe1c", "src": "hda", "uuid": "8e975945-148a-4234-9c24-188021171e22"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "157499d327befe1c", "src": "hda", "uuid": "8e975945-148a-4234-9c24-188021171e22"}, "track_groups_0|data_tracks_0|data_format|annotation2": {"id": "f1a9d9eba899dec5", "src": "hda", "uuid": "e1b7ddd4-4ccc-45c0-8b31-4355ba54a9b6"}, "track_groups_0|data_tracks_0|data_format|annotation3": {"id": "6be692895ae06cac", "src": "hda", "uuid": "de560582-71d2-4146-bcfa-d16c99a9094b"}, "track_groups_0|data_tracks_0|data_format|annotation4": {"id": "33e24f900cb076cb", "src": "hda", "uuid": "84699dfc-7ae5-4799-8bec-98ae16d599c9"}, "track_groups_1|data_tracks_0|data_format|annotation": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_1|data_tracks_0|data_format|annotation1": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_0|data_format|annotation": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_0|data_format|annotation1": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_1|data_format|annotation": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_1|data_format|annotation1": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_2|data_format|annotation": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_2|data_format|annotation1": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_3|data_format|annotation": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_2|data_tracks_3|data_format|annotation1": {"id": "1705eea1fb43e55b", "src": "hda", "uuid": "a812c6a5-0950-4de6-aea7-a50af2a6529e"}, "track_groups_3|data_tracks_0|data_format|annotation": {"id": "8bd04279d51376b3", "src": "hda", "uuid": "3675266f-4d20-4c2d-9482-98656abf6859"}, "track_groups_3|data_tracks_0|data_format|annotation1": {"id": "8bd04279d51376b3", "src": "hda", "uuid": "3675266f-4d20-4c2d-9482-98656abf6859"}, "track_groups_3|data_tracks_1|data_format|annotation": {"id": "047b421f54b03370", "src": "hda", "uuid": "09149cb4-bb95-4819-8da7-353524d518a5"}, "track_groups_3|data_tracks_1|data_format|annotation1": {"id": "047b421f54b03370", "src": "hda", "uuid": "09149cb4-bb95-4819-8da7-353524d518a5"}}, "outputs": {"output": {"id": "cc56dab6b7ee2160", "src": "hda", "uuid": "d948342e-ce67-4433-80ef-7e1c33dcc6e8"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing Auto Coloured / A.gff\nINFO:jbrowse:Processing Auto Coloured / B.gff\nINFO:jbrowse:Processing Auto Coloured / C.gff\nINFO:jbrowse:Processing Auto Coloured / D.gff\nINFO:jbrowse:Processing Ignore Scale / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Realistic / interpro.gff\nINFO:jbrowse:Processing Realistic / 2.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO:jbrowse:Processing Auto Coloured / A.gff\nINFO:jbrowse:Processing Auto Coloured / B.gff\nINFO:jbrowse:Processing Auto Coloured / C.gff\nINFO:jbrowse:Processing Auto Coloured / D.gff\nINFO:jbrowse:Processing Ignore Scale / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Realistic / interpro.gff\nINFO:jbrowse:Processing Realistic / 2.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:15:47", "plugin": "core", "name": "end_epoch", "raw_value": "1726146947.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:15:44", "plugin": "core", "name": "start_epoch", "raw_value": "1726146944.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-4", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 4, "time_seconds": 35.60929465293884, "inputs": {"reference_genome|genome": {"src": "hda", "id": "c2a8a8c5b1307d33"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With menu or index", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "df42f93874a490b6"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_action": "iframeDialog", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_label": "Some menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_title": "Frame title", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_icon": "dijitIconNewTask", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_action": "newWindow", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_label": "Another menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_title": "Frame title 2", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_0|data_tracks_1|data_format|annotation": {"src": "hda", "id": "df42f93874a490b6"}, "track_groups_0|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_1|data_format|index": true, "track_groups_0|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "4fc6e5e22549ed60", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:16:32.791982", "create_time": "2024-09-12T13:16:17.442873", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-cc26b", "command_line": "mkdir -p /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751_files && cp /galaxy/server/database/jobs_directory/000/157/configs/tmp6o_mfd9h /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751_files /galaxy/server/database/jobs_directory/000/157/configs/tmp6o_mfd9h && cp /galaxy/server/database/jobs_directory/000/157/configs/tmpcdut7beg /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751.dat; cp /galaxy/server/database/jobs_directory/000/157/configs/tmp6o_mfd9h /galaxy/server/database/objects/b/3/f/dataset_b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With menu or index\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 186, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_icon\": \"dijitIconNewTask\", \"menu_label\": \"Some menu item\", \"menu_title\": \"Frame title\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}, {\"__index__\": 1, \"menu_action\": \"newWindow\", \"menu_icon\": \"dijitIconBookmark\", \"menu_label\": \"Another menu item\", \"menu_title\": \"Frame title 2\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}]}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 186, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": true, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 185, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "c2a8a8c5b1307d33", "src": "hda", "uuid": "5335f8c6-dee0-4669-8370-99caba3e7062"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "df42f93874a490b6", "src": "hda", "uuid": "12886cb2-dc6a-49ec-8871-d685f79bb766"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "df42f93874a490b6", "src": "hda", "uuid": "12886cb2-dc6a-49ec-8871-d685f79bb766"}, "track_groups_0|data_tracks_1|data_format|annotation": {"id": "df42f93874a490b6", "src": "hda", "uuid": "12886cb2-dc6a-49ec-8871-d685f79bb766"}, "track_groups_0|data_tracks_1|data_format|annotation1": {"id": "df42f93874a490b6", "src": "hda", "uuid": "12886cb2-dc6a-49ec-8871-d685f79bb766"}}, "outputs": {"output": {"id": "7ab97d21cad04356", "src": "hda", "uuid": "b3f7d5e7-4e99-4564-a9bf-6a0e8da4a751"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:16:21", "plugin": "core", "name": "end_epoch", "raw_value": "1726146981.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:16:20", "plugin": "core", "name": "start_epoch", "raw_value": "1726146980.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-5", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 5, "time_seconds": 31.434343576431274, "inputs": {"reference_genome|genome": {"src": "hda", "id": "691abf4abca3f943"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With canvas config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "f817251fca68a917"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|transcriptType": "transcript", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|subParts": "exon", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|impliedUTRs": true, "track_groups_0|data_tracks_0|data_format|track_config|track_class": "JBrowse/View/Track/CanvasFeatures", "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "a532d0d970ae9556", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:17:04.362101", "create_time": "2024-09-12T13:16:51.974442", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-mcl8q", "command_line": "mkdir -p /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41_files && cp /galaxy/server/database/jobs_directory/000/160/configs/tmpxs4sin6v /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41_files /galaxy/server/database/jobs_directory/000/160/configs/tmpxs4sin6v && cp /galaxy/server/database/jobs_directory/000/160/configs/tmpt06hjvjp /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41.dat; cp /galaxy/server/database/jobs_directory/000/160/configs/tmpxs4sin6v /galaxy/server/database/objects/9/d/1/dataset_9d199d4c-daa8-47e1-b4e5-ff491eebda41.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With canvas config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 189, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": false, \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": false}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 0, \"canvas_options\": {\"impliedUTRs\": true, \"subParts\": \"exon\", \"transcriptType\": \"transcript\"}, \"track_class\": \"JBrowse/View/Track/CanvasFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 188, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "691abf4abca3f943", "src": "hda", "uuid": "fb7e893a-b842-4fcf-b154-cd4a5a16fa9b"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "f817251fca68a917", "src": "hda", "uuid": "12e7fdf7-a36b-460d-aee8-22d13fd4d43f"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "f817251fca68a917", "src": "hda", "uuid": "12e7fdf7-a36b-460d-aee8-22d13fd4d43f"}}, "outputs": {"output": {"id": "8476f0905d295047", "src": "hda", "uuid": "9d199d4c-daa8-47e1-b4e5-ff491eebda41"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:16:54", "plugin": "core", "name": "end_epoch", "raw_value": "1726147014.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:16:53", "plugin": "core", "name": "start_epoch", "raw_value": "1726147013.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-6", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 6, "time_seconds": 10.458668231964111, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "jbrowse/1.16.11+galaxy1-7", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 7, "time_seconds": 33.727522134780884, "inputs": {"reference_genome|genome": {"src": "hda", "id": "581cdae216c6f61a"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Auto Coloured", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "463dbf7d65e178eb"}, "track_groups_0|data_tracks_0|data_format|data_format_select": "pileup", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "86bca9ae0d4021b1", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:17:48.766824", "create_time": "2024-09-12T13:17:34.999452", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-jbg4c", "command_line": "mkdir -p /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277_files && cp /galaxy/server/database/jobs_directory/000/165/configs/tmpfdzwd50p /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277_files /galaxy/server/database/jobs_directory/000/165/configs/tmpfdzwd50p && cp /galaxy/server/database/jobs_directory/000/165/configs/tmpexgo1yvs /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277.dat; cp /galaxy/server/database/jobs_directory/000/165/configs/tmpfdzwd50p /galaxy/server/database/objects/e/4/9/dataset_e495b71f-7ef3-4a2d-b522-0f1e2ae2d277.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Auto Coloured\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 3, \"annotation\": {\"values\": [{\"id\": 194, \"src\": \"hda\"}]}, \"auto_snp\": false, \"chunkSizeLimit\": \"5000000\", \"data_format_select\": \"pileup\", \"jb_custom_config\": {\"option\": []}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 193, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "581cdae216c6f61a", "src": "hda", "uuid": "75e6bc1e-c1cd-4f26-a0a0-7653d21f1372"}, "track_groups_0|data_tracks_0|data_format|annotation": {"id": "463dbf7d65e178eb", "src": "hda", "uuid": "770714e4-2cfe-4e99-ab4d-71a3e1cd3534"}, "track_groups_0|data_tracks_0|data_format|annotation1": {"id": "463dbf7d65e178eb", "src": "hda", "uuid": "770714e4-2cfe-4e99-ab4d-71a3e1cd3534"}}, "outputs": {"output": {"id": "bdef8cc29f7f13e5", "src": "hda", "uuid": "e495b71f-7ef3-4a2d-b522-0f1e2ae2d277"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:jbrowse:Processing Auto Coloured / merlin-sample.bam\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stderr": "INFO:jbrowse:Processing Auto Coloured / merlin-sample.bam\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:17:38", "plugin": "core", "name": "end_epoch", "raw_value": "1726147058.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:17:37", "plugin": "core", "name": "start_epoch", "raw_value": "1726147057.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-8", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 8, "time_seconds": 82.6112699508667, "inputs": {"reference_genome|genome_type_select": "indexed", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "699e2082416ee2d7", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:19:11.381884", "create_time": "2024-09-12T13:17:49.406346", "galaxy_version": "23.1", "command_version": "jbrowse.py 0.8.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-bsxx7", "command_line": "mkdir -p /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e_files && cp /galaxy/server/database/jobs_directory/000/166/configs/tmptmt_gbdz /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e_files /galaxy/server/database/jobs_directory/000/166/configs/tmptmt_gbdz && cp /galaxy/server/database/jobs_directory/000/166/configs/tmp1mjmpwca /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e.dat; cp /galaxy/server/database/jobs_directory/000/166/configs/tmptmt_gbdz /galaxy/server/database/objects/1/e/3/dataset_1e374b71-5c1d-4263-8ad4-8644a33ccd5e.dat", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 0, \"genome_type_select\": \"indexed\", \"genomes\": \"apiMel4\"}"}, "inputs": {}, "outputs": {"output": {"id": "7f25065ae839633b", "src": "hda", "uuid": "1e374b71-5c1d-4263-8ad4-8644a33ccd5e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "job_stdout": "", "job_stderr": "", "stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "66.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:18:57", "plugin": "core", "name": "end_epoch", "raw_value": "1726147137.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:17:51", "plugin": "core", "name": "start_epoch", "raw_value": "1726147071.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected\nExpected text 'merlin.fa' in output ('\n\n \n 1\n \n \n \n s\n \n \n \n 20\n\n true\n \n true\n true\n true\n true\n false\n \n http://localhost:8080\n \n \n \n \n\n')"], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-9", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 9, "time_seconds": 22.64787745475769, "inputs": {"reference_genome|genome": {"src": "hda", "id": "e86b9dfb6d985c8c"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "External endpoints", "track_groups_0|data_tracks_0|data_format|url": "http://example.org.external/rest_api/", "track_groups_0|data_tracks_0|data_format|label": "Rest api", "track_groups_0|data_tracks_0|data_format|data_format_select": "rest", "track_groups_0|data_tracks_1|data_format|url": "http://example.org.external/sparql/", "track_groups_0|data_tracks_1|data_format|label": "Sparql endpoint", "track_groups_0|data_tracks_1|data_format|query": " DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }", "track_groups_0|data_tracks_1|data_format|data_format_select": "sparql", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "c18cd423ba921e33", "state": "error", "exit_code": null, "update_time": "2024-09-12T13:19:34.271477", "create_time": "2024-09-12T13:19:28.591671", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-4grm7", "command_line": "mkdir -p /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files && cp /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4_files /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 && cp /galaxy/server/database/jobs_directory/000/168/configs/tmpe_v1eztl /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat; cp /galaxy/server/database/jobs_directory/000/168/configs/tmph_ookhs2 /galaxy/server/database/objects/4/7/3/dataset_4732c9b8-5134-40db-93aa-e15a5b2e43b4.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"External endpoints\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 5, \"data_format_select\": \"rest\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Rest api\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/rest_api/\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 6, \"data_format_select\": \"sparql\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Sparql endpoint\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"query\": \" DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/sparql/\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 197, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"reference_genome|genome": {"id": "e86b9dfb6d985c8c", "src": "hda", "uuid": "2ed33cef-cd23-4e80-84be-8480e7ce1da5"}}, "outputs": {"output": {"id": "a5948005d8a94f42", "src": "hda", "uuid": "4732c9b8-5134-40db-93aa-e15a5b2e43b4"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "lofreq_call/2.1.5+galaxy2-0", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 0, "time_seconds": 38.60614800453186, "inputs": {"reads": {"src": "hda", "id": "2dffea7156c2f946"}, "reference_source|ref": {"src": "hda", "id": "4b01e22ab2d6bf1d"}, "reference_source|ref_selector": "history"}, "job": {"model_class": "Job", "id": "ac547a96e883f049", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:10:23.818336", "create_time": "2024-09-12T13:10:04.556408", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "45fb41c325e9adff", "external_id": "gxy-4szbv", "command_line": "ln -s '/galaxy/server/database/objects/7/7/b/dataset_77b907a7-574a-49e6-977b-68cba0624d9f.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/5/9/3/dataset_5933cea0-c94c-4c28-86aa-cea36ef33791.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/b/f/7/metadata_bf747e1a-a9de-4833-8eb1-c036ece3d644.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 150, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "2dffea7156c2f946", "src": "hda", "uuid": "5933cea0-c94c-4c28-86aa-cea36ef33791"}, "reference_source|ref": {"id": "4b01e22ab2d6bf1d", "src": "hda", "uuid": "77b907a7-574a-49e6-977b-68cba0624d9f"}}, "outputs": {"variants": {"id": "a32388ba8406a825", "src": "hda", "uuid": "ce3cfd93-1566-4706-a6a0-8774b6085e23"}}, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 13:10:11,245]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 13:10:11,256]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:10:12,980]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/121/tmp/lofreq2_call_parallelbegftnbd/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2024-09-12 13:10:11,245]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 13:10:11,256]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:10:12,980]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/121/tmp/lofreq2_call_parallelbegftnbd/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:10:13", "plugin": "core", "name": "end_epoch", "raw_value": "1726146613.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:10:11", "plugin": "core", "name": "start_epoch", "raw_value": "1726146611.0000000"}, {"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": "lofreq_call/2.1.5+galaxy2-1", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 1, "time_seconds": 32.71448373794556, "inputs": {"reads": {"src": "hda", "id": "ff7864dc2243e76c"}, "reference_source|ref": {"src": "hda", "id": "8fb27de822c69f14"}, "reference_source|ref_selector": "history", "call_control|set_call_options": "yes"}, "job": {"model_class": "Job", "id": "e6356d72fa49a643", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:10:56.705976", "create_time": "2024-09-12T13:10:43.152298", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "45fb41c325e9adff", "external_id": "gxy-k4rj5", "command_line": "ln -s '/galaxy/server/database/objects/d/4/d/dataset_d4dfb13b-9d55-416e-8767-f0b93119a420.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/8/5/c/dataset_85c05234-1333-4459-bdb1-047d5dde965f.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/2/7/5/metadata_27594236-acce-4826-a976-aec022248217.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 1, \"align_quals\": {\"alnqual\": {\"__current_case__\": 0, \"alnqual_choice\": {\"__current_case__\": 1, \"alnquals_to_use\": \"\", \"extended_baq\": true}, \"use_alnqual\": \"\"}}, \"bc_quals\": {\"alt_bq\": {\"__current_case__\": 0, \"modify\": \"\"}, \"min_alt_bq\": \"6\", \"min_bq\": \"6\"}, \"coverage\": {\"max_depth\": \"1000000\", \"min_cov\": \"1\"}, \"joint_qual\": {\"def_alt_jq\": \"0\", \"min_alt_jq\": \"0\", \"min_jq\": \"0\"}, \"map_quals\": {\"min_mq\": \"0\", \"use_mq\": {\"__current_case__\": 0, \"max_mq\": \"255\", \"no_mq\": \"\"}}, \"pe\": {\"use_orphan\": false}, \"set_call_options\": \"yes\", \"source_qual\": {\"use_src_qual\": {\"__current_case__\": 0, \"src_qual\": \"\"}}}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "ff7864dc2243e76c", "src": "hda", "uuid": "85c05234-1333-4459-bdb1-047d5dde965f"}, "reference_source|ref": {"id": "8fb27de822c69f14", "src": "hda", "uuid": "d4dfb13b-9d55-416e-8767-f0b93119a420"}}, "outputs": {"variants": {"id": "b2a75b95a3a0943f", "src": "hda", "uuid": "95fb20f0-16db-4722-a169-c2e195de5ff3"}}, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 13:10:45,273]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 13:10:45,284]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:10:47,060]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/124/tmp/lofreq2_call_parallelpppa028l/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2024-09-12 13:10:45,273]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 13:10:45,284]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:10:47,060]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/124/tmp/lofreq2_call_parallelpppa028l/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:10:47", "plugin": "core", "name": "end_epoch", "raw_value": "1726146647.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:10:45", "plugin": "core", "name": "start_epoch", "raw_value": "1726146645.0000000"}, {"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": "lofreq_call/2.1.5+galaxy2-2", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 2, "time_seconds": 35.805041551589966, "inputs": {"reads": {"src": "hda", "id": "aad2d829deed67c5"}, "reference_source|ref": {"src": "hda", "id": "44efe9bb9ae12026"}, "reference_source|ref_selector": "history", "call_control|source_qual|use_src_qual|def_nm_q": "40", "call_control|source_qual|use_src_qual|ign_vcf": {"src": "hda", "id": "4fc6e5e22549ed60"}, "call_control|source_qual|use_src_qual|src_qual": "--src-qual", "call_control|set_call_options": "yes"}, "job": {"model_class": "Job", "id": "1381c17b42c4ef57", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:11:32.590636", "create_time": "2024-09-12T13:11:19.030457", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "45fb41c325e9adff", "external_id": "gxy-mjzmw", "command_line": "ln -s '/galaxy/server/database/objects/a/1/6/dataset_a160720b-e062-4f72-9197-c5b80f55b0ba.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/c/4/e/dataset_c4ef6f65-10b5-450e-9b43-ef723818cf0b.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/5/b/4/metadata_5b480184-78f8-4bdd-863b-723c6c2687f2.dat' reads.bam.bai && ln -s '/galaxy/server/database/objects/1/a/6/dataset_1a6993a6-b3a3-4df0-a8dc-4484467b2b35.dat' ign0.vcf && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf 'ign0.vcf' --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 1, \"align_quals\": {\"alnqual\": {\"__current_case__\": 0, \"alnqual_choice\": {\"__current_case__\": 1, \"alnquals_to_use\": \"\", \"extended_baq\": true}, \"use_alnqual\": \"\"}}, \"bc_quals\": {\"alt_bq\": {\"__current_case__\": 0, \"modify\": \"\"}, \"min_alt_bq\": \"6\", \"min_bq\": \"6\"}, \"coverage\": {\"max_depth\": \"1000000\", \"min_cov\": \"1\"}, \"joint_qual\": {\"def_alt_jq\": \"0\", \"min_alt_jq\": \"0\", \"min_jq\": \"0\"}, \"map_quals\": {\"min_mq\": \"0\", \"use_mq\": {\"__current_case__\": 0, \"max_mq\": \"255\", \"no_mq\": \"\"}}, \"pe\": {\"use_orphan\": false}, \"set_call_options\": \"yes\", \"source_qual\": {\"use_src_qual\": {\"__current_case__\": 1, \"def_nm_q\": \"40\", \"ign_vcf\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"src_qual\": \"--src-qual\"}}}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 156, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "aad2d829deed67c5", "src": "hda", "uuid": "c4ef6f65-10b5-450e-9b43-ef723818cf0b"}, "reference_source|ref": {"id": "44efe9bb9ae12026", "src": "hda", "uuid": "a160720b-e062-4f72-9197-c5b80f55b0ba"}, "call_control|source_qual|use_src_qual|ign_vcf": {"id": "4fc6e5e22549ed60", "src": "hda", "uuid": "1a6993a6-b3a3-4df0-a8dc-4484467b2b35"}, "call_control|source_qual|use_src_qual|ign_vcf1": {"id": "4fc6e5e22549ed60", "src": "hda", "uuid": "1a6993a6-b3a3-4df0-a8dc-4484467b2b35"}}, "outputs": {"variants": {"id": "625eb35b22060e38", "src": "hda", "uuid": "297aed2b-d17d-43fa-a7fa-cace109271fc"}}, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 13:11:20,912]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 13:11:20,924]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:11:22,934]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/128/tmp/lofreq2_call_parallelhmyee2rp/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2024-09-12 13:11:20,912]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 13:11:20,924]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:11:22,934]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/128/tmp/lofreq2_call_parallelhmyee2rp/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:11:23", "plugin": "core", "name": "end_epoch", "raw_value": "1726146683.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:11:20", "plugin": "core", "name": "start_epoch", "raw_value": "1726146680.0000000"}, {"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": "lofreq_call/2.1.5+galaxy2-3", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 3, "time_seconds": 34.080294609069824, "inputs": {"reads": {"src": "hda", "id": "400c328259657a59"}, "reference_source|ref": {"src": "hda", "id": "a532d0d970ae9556"}, "reference_source|ref_selector": "history", "filter_control|filter_type": "set_all_off"}, "job": {"model_class": "Job", "id": "c33fcc83aebe3540", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:12:06.623955", "create_time": "2024-09-12T13:11:52.065370", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "45fb41c325e9adff", "external_id": "gxy-7xcfq", "command_line": "ln -s '/galaxy/server/database/objects/b/c/9/dataset_bc911942-148e-453d-90e2-c46f6f8a553e.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/7/6/0/dataset_760d2696-8cde-4a6d-baca-67e0612593ca.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/2/5/7/metadata_25717292-b118-40e0-ba4d-2b7dae5213e0.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "400c328259657a59", "src": "hda", "uuid": "760d2696-8cde-4a6d-baca-67e0612593ca"}, "reference_source|ref": {"id": "a532d0d970ae9556", "src": "hda", "uuid": "bc911942-148e-453d-90e2-c46f6f8a553e"}}, "outputs": {"variants": {"id": "051dc5929d40d789", "src": "hda", "uuid": "9c5336fe-ec44-4181-ac65-9cfc7d68e45f"}}, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 13:11:54,224]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 13:11:54,235]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:11:56,029]: Copying concatenated vcf file to final destination\nset_all_off\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2024-09-12 13:11:54,224]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 13:11:54,235]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 13:11:56,029]: Copying concatenated vcf file to final destination\nset_all_off\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:11:56", "plugin": "core", "name": "end_epoch", "raw_value": "1726146716.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:11:54", "plugin": "core", "name": "start_epoch", "raw_value": "1726146714.0000000"}, {"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": "lofreq_call/2.1.5+galaxy2-4", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 4, "time_seconds": 34.94112944602966, "inputs": {"reads": {"src": "hda", "id": "f883ecbb9b4f587d"}, "reference_source|ref": {"src": "hda", "id": "57899371865de695"}, "reference_source|ref_selector": "history", "variant_types": "--call-indels --only-indels", "filter_control|filter_type": "set_all_off"}, "job": {"model_class": "Job", "id": "98e036e4ea2088a4", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:12:41.519949", "create_time": "2024-09-12T13:12:25.676961", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "45fb41c325e9adff", "external_id": "gxy-sbnf2", "command_line": "ln -s '/galaxy/server/database/objects/0/a/9/dataset_0a9f0e0a-12ef-4214-b499-654afca7a85a.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/0/8/e/dataset_08e3cac9-2e3a-4291-b16f-838fb39258c2.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/3/a/c/metadata_3ace4b26-6eb9-4875-b3fe-8acc9b200551.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"--call-indels --only-indels\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 163, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "f883ecbb9b4f587d", "src": "hda", "uuid": "08e3cac9-2e3a-4291-b16f-838fb39258c2"}, "reference_source|ref": {"id": "57899371865de695", "src": "hda", "uuid": "0a9f0e0a-12ef-4214-b499-654afca7a85a"}}, "outputs": {"variants": {"id": "265729caa41a1863", "src": "hda", "uuid": "120209da-0d47-4e84-910d-ec4f693ff00e"}}, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 13:12:28,689]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 13:12:28,702]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2024-09-12 13:12:31,379]: Copying concatenated vcf file to final destination\nset_all_off\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2024-09-12 13:12:28,689]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 13:12:28,702]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2024-09-12 13:12:31,379]: Copying concatenated vcf file to final destination\nset_all_off\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:12:31", "plugin": "core", "name": "end_epoch", "raw_value": "1726146751.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:12:28", "plugin": "core", "name": "start_epoch", "raw_value": "1726146748.0000000"}, {"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": "multiqc/1.9+galaxy1-0", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 0, "time_seconds": 26.17760705947876, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-1", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 1, "time_seconds": 65.9575560092926, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-2", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 2, "time_seconds": 12.314083814620972, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-3", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 3, "time_seconds": 131.7817714214325, "inputs": {"results_0|software_cond|plot_type": "linegraph", "results_0|software_cond|section_name": "BPC", "results_0|software_cond|title": "Base peak chromatogram", "results_0|software_cond|description": "Sum of intensity (Y) of the most intense peaks at each retention time(X)", "results_0|software_cond|xlab": "Retention Time", "results_0|software_cond|ylab": "Base Peak Intensity", "results_0|software_cond|input": [{"src": "hda", "id": "436c5a64dec43345"}, {"src": "hda", "id": "57c182ccb96215d8"}], "results_0|software_cond|software": "custom_content"}, "job": {"model_class": "Job", "id": "779365dce838fb80", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T12:55:18.008149", "create_time": "2024-09-12T12:54:23.103273", "galaxy_version": "23.1", "command_version": "multiqc, version 1.9", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-dw7wh", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/custom_content_0 && ln -s '/galaxy/server/database/objects/2/4/f/dataset_24f805b6-5b52-4e20-a439-529a0449687b.dat' 'multiqc_WDir/custom_content_0/file_0_0' && more /galaxy/server/database/objects/2/4/f/dataset_24f805b6-5b52-4e20-a439-529a0449687b.dat && ln -s '/galaxy/server/database/objects/f/d/b/dataset_fdb968eb-e622-496d-ad5f-06d9bab16eff.dat' 'multiqc_WDir/custom_content_0/file_0_1' && more /galaxy/server/database/objects/f/d/b/dataset_fdb968eb-e622-496d-ad5f-06d9bab16eff.dat && multiqc multiqc_WDir --filename \"report\" --config '/galaxy/server/database/jobs_directory/000/61/configs/tmpy7npc9fe'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"\"", "title": "\"\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 32, \"description\": \"Sum of intensity (Y) of the most intense peaks at each retention time(X)\", \"input\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}, {\"id\": 60, \"src\": \"hda\"}]}, \"plot_type\": \"linegraph\", \"section_name\": \"BPC\", \"software\": \"custom_content\", \"title\": \"Base peak chromatogram\", \"xlab\": \"Retention Time\", \"ylab\": \"Base Peak Intensity\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "436c5a64dec43345", "src": "hda", "uuid": "24f805b6-5b52-4e20-a439-529a0449687b"}, "results_0|software_cond|input1": {"id": "436c5a64dec43345", "src": "hda", "uuid": "24f805b6-5b52-4e20-a439-529a0449687b"}, "results_0|software_cond|input2": {"id": "57c182ccb96215d8", "src": "hda", "uuid": "fdb968eb-e622-496d-ad5f-06d9bab16eff"}}, "outputs": {"html_report": {"id": "779365dce838fb80", "src": "hda", "uuid": "4c850119-0ad5-43ba-a065-19942a8a5841"}, "__new_primary_file_stats|sources__": {"id": "ecc08807fdb2a45f", "src": "hda", "uuid": "06d0d4a2-f5f4-4d73-ac05-b1cd44fef65d"}}, "output_collections": {"stats": {"id": "45fb41c325e9adff", "src": "hdca"}}, "tool_stdout": 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"tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/61/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/61/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "stdout": 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"job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-12 12:55:05", "plugin": "core", "name": "end_epoch", "raw_value": "1726145705.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 12:55:00", "plugin": "core", "name": "start_epoch", "raw_value": "1726145700.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output html_report: Test output file (report_manual_custom_content.html) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "multiqc/1.9+galaxy1-4", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 4, "time_seconds": 44.23818111419678, "inputs": {"results_0|software_cond|output_0|type": "data", "results_0|software_cond|output_0|input": [{"src": "hda", "id": "375f09a9538356a1"}, {"src": "hda", "id": "7b5b892ecab82f4f"}], "results_0|software_cond|software": "fastqc", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true}, "job": {"model_class": "Job", "id": "7b5b892ecab82f4f", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T12:56:01.904049", "create_time": "2024-09-12T12:55:38.098737", "galaxy_version": "23.1", "command_version": "multiqc, version 1.9", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-tsxnd", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastqc_0 && mkdir 'multiqc_WDir/fastqc_0/data_0' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/galaxy/server/database/objects/6/a/e/dataset_6ae365f2-fa59-4bfa-8285-e06f53c2ef2f.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/galaxy/server/database/objects/d/d/1/dataset_dd1ee562-0bfe-4280-b4b3-307414b8c412.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "true", "flat": "true", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 63, \"src\": \"hda\"}, {\"id\": 64, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]"}, "inputs": {"results_0|software_cond|output_0|input": {"id": "375f09a9538356a1", "src": "hda", "uuid": "6ae365f2-fa59-4bfa-8285-e06f53c2ef2f"}, "results_0|software_cond|output_0|input1": {"id": "375f09a9538356a1", "src": "hda", "uuid": "6ae365f2-fa59-4bfa-8285-e06f53c2ef2f"}, "results_0|software_cond|output_0|input2": {"id": "7b5b892ecab82f4f", "src": "hda", "uuid": "dd1ee562-0bfe-4280-b4b3-307414b8c412"}}, "outputs": {"html_report": {"id": "edc9d596a056686d", "src": "hda", "uuid": "aa2f20a8-f2c3-4309-8fe6-5d159c76ea1c"}, "__new_primary_file_stats|sources__": {"id": "c5cabb4145f8077b", "src": "hda", "uuid": "56ddea83-f0a3-40b6-bd69-4d3488db595b"}, "__new_primary_file_plots|fastqc_per_base_n_content_plot_1__": {"id": "02250aa4de4cbc16", "src": "hda", "uuid": 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"", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/64/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "12 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "12.0000000"}, {"title": "Job End Time", "value": "2024-09-12 12:55:52", "plugin": "core", "name": "end_epoch", "raw_value": "1726145752.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 12:55:40", "plugin": "core", "name": "start_epoch", "raw_value": "1726145740.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-5", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 5, "time_seconds": 34.77101802825928, "inputs": {"results_0|software_cond|input": {"src": "hda", "id": "63bddd09d6f30036"}, "results_0|software_cond|software": "pycoqc", "title": "Title of the report", "comment": "Commment for the report"}, "job": {"model_class": "Job", "id": "02250aa4de4cbc16", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T12:56:37.204617", "create_time": "2024-09-12T12:56:20.518074", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "45fb41c325e9adff", "external_id": "gxy-b468v", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/pycoqc_0 && grep -q '\"pycoqc\":' /galaxy/server/database/objects/9/8/3/dataset_9830ce18-7560-4f15-a2e5-1bdc1196173b.dat || die \"Module 'pycoqc: '\"pycoqc\":' not found in the file 'pycoqc_json'\" && ln -s '/galaxy/server/database/objects/9/8/3/dataset_9830ce18-7560-4f15-a2e5-1bdc1196173b.dat' 'multiqc_WDir/pycoqc_0/pycoqc_json' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\"", "traceback": null, "params": {"__input_ext": "\"json\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 19, \"input\": {\"values\": [{\"id\": 76, \"src\": \"hda\"}]}, \"software\": \"pycoqc\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "63bddd09d6f30036", "src": "hda", "uuid": "9830ce18-7560-4f15-a2e5-1bdc1196173b"}, "results_0|software_cond|input1": {"id": "63bddd09d6f30036", "src": "hda", "uuid": "9830ce18-7560-4f15-a2e5-1bdc1196173b"}}, "outputs": {"__new_primary_file_stats|sources__": {"id": "96bac482d8b094fa", "src": "hda", "uuid": "a6f90dc1-204b-419b-8bed-777051be881f"}, "html_report": {"id": "2e58c3969419a55a", "src": "hda", "uuid": "cc0828f6-4895-4503-a2f4-f99c8168bf48"}, "__new_primary_file_stats|general_stats__": {"id": "11e89e0c17d36cde", "src": "hda", "uuid": "8e7c30ec-94a3-46bb-8ce7-9023ac03c9c8"}}, "output_collections": {"stats": {"id": "987935bc9fe4a326", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/66/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/66/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-12 12:56:27", "plugin": "core", "name": "end_epoch", "raw_value": "1726145787.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 12:56:22", "plugin": "core", "name": "start_epoch", "raw_value": "1726145782.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "nanoplot/1.43.0+galaxy0-0", "has_data": true, "data": {"tool_id": "nanoplot", "tool_version": "1.43.0+galaxy0", "test_index": 0, "time_seconds": 80.22500658035278, "inputs": {"mode|reads|files": {"src": "hda", "id": "41b4826423ace419"}, "mode|reads|type": "fastq_rich", "mode|choice": "batch", "filter|downsample": "800", "customization|plots": "kde"}, "job": {"model_class": "Job", "id": "5bc6dfeed7ce6fa3", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:05:22.836130", "create_time": "2024-09-12T13:04:22.910973", "galaxy_version": "23.1", "command_version": "NanoPlot 1.43.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0", "history_id": "45fb41c325e9adff", "external_id": "gxy-zf6xn", "command_line": "ln -s '/galaxy/server/database/objects/8/5/4/dataset_854eea0c-b07e-41b5-a964-6284ca75106b.dat' './read_0.fastq.gz' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --fastq_rich read_0.fastq.gz --downsample 800 --plots kde -o '.' && >&2 cat *log", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "customization": "{\"N50\": false, \"color\": null, \"plots\": \"kde\"}", "filter": "{\"alength\": false, \"barcoded\": false, \"downsample\": \"800\", \"drop_outliers\": false, \"loglength\": false, \"maxlength\": \"\", \"minlength\": \"\", \"minqual\": \"\", \"no_supplementary\": false, \"percentqual\": false, \"readtype\": null, \"runtime_until\": \"\"}", "mode": "{\"__current_case__\": 0, \"choice\": \"batch\", \"reads\": {\"__current_case__\": 2, \"files\": {\"values\": [{\"id\": 126, \"src\": \"hda\"}]}, \"type\": \"fastq_rich\"}}"}, "inputs": {"mode|reads|files": {"id": "41b4826423ace419", "src": "hda", "uuid": "854eea0c-b07e-41b5-a964-6284ca75106b"}}, "outputs": {"output_html": {"id": "2ab81e2d4b71799c", "src": "hda", "uuid": "58a742af-9543-4b59-a3cf-fe4f6b5a3bf5"}, "nanostats": {"id": "1381c17b42c4ef57", "src": "hda", "uuid": "397d2452-4b5b-4391-bafa-b6f6cb208f7b"}, "nanostats_post_filtering": {"id": "91d1501bd87ed579", "src": "hda", "uuid": "8db2ad6e-8ac7-4cf7-a892-1e5051c7d802"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "2024-09-12 13:05:02,829 NanoPlot 1.43.0 started with arguments Namespace(threads=2, verbose=False, store=False, raw=False, huge=False, outdir='.', no_static=True, prefix='', tsv_stats=True, only_report=False, info_in_report=False, maxlength=None, minlength=None, drop_outliers=False, downsample=800, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='#4CB391', colormap='Greens', format=['png'], plots=['kde'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=False, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=None, fasta=None, fastq_rich=['read_0.fastq.gz'], fastq_minimal=None, summary=None, bam=None, ubam=None, cram=None, pickle=None, feather=None, path='./')\n2024-09-12 13:05:02,829 Python version is: 3.12.5 | packaged by conda-forge | (main, Aug 8 2024, 18:36:51) [GCC 12.4.0]\n2024-09-12 13:05:02,874 Nanoget: Starting to collect statistics from rich fastq file.\n2024-09-12 13:05:02,876 Nanoget: Decompressing gzipped fastq read_0.fastq.gz\n2024-09-12 13:05:03,803 Reduced DataFrame memory usage from 0.042937278747558594Mb to 0.042937278747558594Mb\n2024-09-12 13:05:03,826 Nanoget: Gathered all metrics of 371 reads\n2024-09-12 13:05:03,846 Calculated statistics\n2024-09-12 13:05:03,847 Using sequenced read lengths for plotting.\n2024-09-12 13:05:03,848 Downsampling the dataset from 371 to 371 reads\n2024-09-12 13:05:03,863 Calculated statistics\n2024-09-12 13:05:03,863 NanoPlot: Valid color #4CB391.\n2024-09-12 13:05:03,864 NanoPlot: Valid colormap Greens.\n2024-09-12 13:05:03,864 NanoPlot: Creating length plots for Read length.\n2024-09-12 13:05:03,865 NanoPlot: Using 371 reads maximum of 393431bp.\n2024-09-12 13:05:04,685 Created length plots\n2024-09-12 13:05:04,686 NanoPlot: Creating Read lengths vs Average read quality plots using 371 reads.\n2024-09-12 13:05:04,718 Created LengthvsQual plot\n2024-09-12 13:05:04,718 Nanoplotter: Creating heatmap of reads per channel using 371 reads.\n2024-09-12 13:05:04,735 Created spatialheatmap for succesfull basecalls.\n2024-09-12 13:05:04,736 Nanoplotter: Creating timeplots using 371 (full) or 371 (subsampled dataset) reads.\n2024-09-12 13:05:04,956 Created timeplots.\n2024-09-12 13:05:04,957 Writing html report.\n2024-09-12 13:05:04,976 Finished!\n", "job_stdout": "", "job_stderr": "", "stderr": "2024-09-12 13:05:02,829 NanoPlot 1.43.0 started with arguments Namespace(threads=2, verbose=False, store=False, raw=False, huge=False, outdir='.', no_static=True, prefix='', tsv_stats=True, only_report=False, info_in_report=False, maxlength=None, minlength=None, drop_outliers=False, downsample=800, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='#4CB391', colormap='Greens', format=['png'], plots=['kde'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=False, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=None, fasta=None, fastq_rich=['read_0.fastq.gz'], fastq_minimal=None, summary=None, bam=None, ubam=None, cram=None, pickle=None, feather=None, path='./')\n2024-09-12 13:05:02,829 Python version is: 3.12.5 | packaged by conda-forge | (main, Aug 8 2024, 18:36:51) [GCC 12.4.0]\n2024-09-12 13:05:02,874 Nanoget: Starting to collect statistics from rich fastq file.\n2024-09-12 13:05:02,876 Nanoget: Decompressing gzipped fastq read_0.fastq.gz\n2024-09-12 13:05:03,803 Reduced DataFrame memory usage from 0.042937278747558594Mb to 0.042937278747558594Mb\n2024-09-12 13:05:03,826 Nanoget: Gathered all metrics of 371 reads\n2024-09-12 13:05:03,846 Calculated statistics\n2024-09-12 13:05:03,847 Using sequenced read lengths for plotting.\n2024-09-12 13:05:03,848 Downsampling the dataset from 371 to 371 reads\n2024-09-12 13:05:03,863 Calculated statistics\n2024-09-12 13:05:03,863 NanoPlot: Valid color #4CB391.\n2024-09-12 13:05:03,864 NanoPlot: Valid colormap Greens.\n2024-09-12 13:05:03,864 NanoPlot: Creating length plots for Read length.\n2024-09-12 13:05:03,865 NanoPlot: Using 371 reads maximum of 393431bp.\n2024-09-12 13:05:04,685 Created length plots\n2024-09-12 13:05:04,686 NanoPlot: Creating Read lengths vs Average read quality plots using 371 reads.\n2024-09-12 13:05:04,718 Created LengthvsQual plot\n2024-09-12 13:05:04,718 Nanoplotter: Creating heatmap of reads per channel using 371 reads.\n2024-09-12 13:05:04,735 Created spatialheatmap for succesfull basecalls.\n2024-09-12 13:05:04,736 Nanoplotter: Creating timeplots using 371 (full) or 371 (subsampled dataset) reads.\n2024-09-12 13:05:04,956 Created timeplots.\n2024-09-12 13:05:04,957 Writing html report.\n2024-09-12 13:05:04,976 Finished!\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "9 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": 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"update_time": "2024-09-12T13:06:06.085492", "create_time": "2024-09-12T13:05:43.667612", "galaxy_version": "23.1", "command_version": "NanoPlot 1.43.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0", "history_id": "45fb41c325e9adff", "external_id": "gxy-r5wlk", "command_line": "ln -s '/galaxy/server/database/objects/4/f/2/dataset_4f2bcdee-25c7-4455-a098-02bcc80b4316.dat' './read_0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/9/6/e/metadata_96e0e222-3d73-48c4-a8be-ccbf413ee512.dat' './read_0.bam.bai' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --bam read_0.bam --maxlength 2000 --color yellow -o '.' && >&2 cat *log", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "customization": "{\"N50\": false, \"color\": \"yellow\", \"plots\": null}", "filter": "{\"alength\": false, \"barcoded\": 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"output_collections": {}, "tool_stdout": "", "tool_stderr": "2024-09-12 13:05:51,866 NanoPlot 1.43.0 started with arguments Namespace(threads=2, verbose=False, store=False, raw=False, huge=False, outdir='.', no_static=True, prefix='', tsv_stats=True, only_report=False, info_in_report=False, maxlength=2000, minlength=None, drop_outliers=False, downsample=None, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='yellow', colormap='Greens', format=['png'], plots=['kde', 'dot'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=False, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=None, fasta=None, fastq_rich=None, fastq_minimal=None, summary=None, bam=['read_0.bam'], ubam=None, cram=None, pickle=None, feather=None, path='./')\n2024-09-12 13:05:51,866 Python version is: 3.12.5 | packaged by conda-forge | (main, Aug 8 2024, 18:36:51) [GCC 12.4.0]\n2024-09-12 13:05:51,912 Nanoget: Starting to collect statistics from bam file read_0.bam.\n2024-09-12 13:05:51,922 Nanoget: Bam file read_0.bam contains 1197 mapped and 40 unmapped reads.\n2024-09-12 13:05:53,665 Nanoget: bam read_0.bam contains 1115 primary alignments.\n2024-09-12 13:05:53,678 Reduced DataFrame memory usage from 0.11804485321044922Mb to 0.11804485321044922Mb\n2024-09-12 13:05:53,696 Nanoget: Gathered all metrics of 1115 reads\n2024-09-12 13:05:53,720 Calculated statistics\n2024-09-12 13:05:53,721 Using sequenced read lengths for plotting.\n2024-09-12 13:05:53,723 Hidding 959 reads longer than 2000bp in length plots.\n2024-09-12 13:05:53,724 NanoPlot: Valid color yellow.\n2024-09-12 13:05:53,725 NanoPlot: Valid colormap Greens.\n2024-09-12 13:05:53,725 NanoPlot: Creating length plots for Read length.\n2024-09-12 13:05:53,726 NanoPlot: Using 156 reads maximum of 1985bp.\n2024-09-12 13:05:54,549 Created length plots\n2024-09-12 13:05:54,550 NanoPlot: Creating Read lengths vs Average read quality plots using 156 reads.\n2024-09-12 13:05:54,672 Created LengthvsQual plot\n2024-09-12 13:05:54,673 NanoPlot: Creating Aligned read lengths vs Sequenced read length plots using 156 reads.\n2024-09-12 13:05:54,772 Created AlignedLength vs Length plot.\n2024-09-12 13:05:54,772 NanoPlot: Creating Read mapping quality vs Average basecall quality plots using 1115 reads.\n2024-09-12 13:05:54,887 Created MapQvsBaseQ plot.\n2024-09-12 13:05:54,888 NanoPlot: Creating Read length vs Read mapping quality plots using 156 reads.\n2024-09-12 13:05:54,983 Created Mapping quality vs read length plot.\n2024-09-12 13:05:54,984 NanoPlot: Creating Percent identity vs Average Base Quality plots using 1115 reads.\n2024-09-12 13:05:55,099 Created Percent ID vs Base quality plot.\n2024-09-12 13:05:55,100 NanoPlot: Creating Aligned read length vs Percent identity plots using 156 reads.\n2024-09-12 13:05:55,280 Created Percent ID vs Length plot\n2024-09-12 13:05:55,280 Writing html report.\n2024-09-12 13:05:55,354 Finished!\n", "job_stdout": "", "job_stderr": "", "stderr": "2024-09-12 13:05:51,866 NanoPlot 1.43.0 started with arguments Namespace(threads=2, verbose=False, store=False, raw=False, huge=False, outdir='.', no_static=True, prefix='', tsv_stats=True, only_report=False, info_in_report=False, maxlength=2000, minlength=None, drop_outliers=False, downsample=None, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='yellow', colormap='Greens', format=['png'], plots=['kde', 'dot'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=False, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=None, fasta=None, fastq_rich=None, fastq_minimal=None, summary=None, bam=['read_0.bam'], ubam=None, cram=None, pickle=None, feather=None, path='./')\n2024-09-12 13:05:51,866 Python version is: 3.12.5 | packaged by conda-forge | (main, Aug 8 2024, 18:36:51) [GCC 12.4.0]\n2024-09-12 13:05:51,912 Nanoget: Starting to collect statistics from bam file read_0.bam.\n2024-09-12 13:05:51,922 Nanoget: Bam file read_0.bam contains 1197 mapped and 40 unmapped reads.\n2024-09-12 13:05:53,665 Nanoget: bam read_0.bam contains 1115 primary alignments.\n2024-09-12 13:05:53,678 Reduced DataFrame memory usage from 0.11804485321044922Mb to 0.11804485321044922Mb\n2024-09-12 13:05:53,696 Nanoget: Gathered all metrics of 1115 reads\n2024-09-12 13:05:53,720 Calculated statistics\n2024-09-12 13:05:53,721 Using sequenced read lengths for plotting.\n2024-09-12 13:05:53,723 Hidding 959 reads longer than 2000bp in length plots.\n2024-09-12 13:05:53,724 NanoPlot: Valid color yellow.\n2024-09-12 13:05:53,725 NanoPlot: Valid colormap Greens.\n2024-09-12 13:05:53,725 NanoPlot: Creating length plots for Read length.\n2024-09-12 13:05:53,726 NanoPlot: Using 156 reads maximum of 1985bp.\n2024-09-12 13:05:54,549 Created length plots\n2024-09-12 13:05:54,550 NanoPlot: Creating Read lengths vs Average read quality plots using 156 reads.\n2024-09-12 13:05:54,672 Created LengthvsQual plot\n2024-09-12 13:05:54,673 NanoPlot: Creating Aligned read lengths vs Sequenced read length plots using 156 reads.\n2024-09-12 13:05:54,772 Created AlignedLength vs Length plot.\n2024-09-12 13:05:54,772 NanoPlot: Creating Read mapping quality vs Average basecall quality plots using 1115 reads.\n2024-09-12 13:05:54,887 Created MapQvsBaseQ plot.\n2024-09-12 13:05:54,888 NanoPlot: Creating Read length vs Read mapping quality plots using 156 reads.\n2024-09-12 13:05:54,983 Created Mapping quality vs read length plot.\n2024-09-12 13:05:54,984 NanoPlot: Creating Percent identity vs Average Base Quality plots using 1115 reads.\n2024-09-12 13:05:55,099 Created Percent ID vs Base quality plot.\n2024-09-12 13:05:55,100 NanoPlot: Creating Aligned read length vs Percent identity plots using 156 reads.\n2024-09-12 13:05:55,280 Created Percent ID vs Length plot\n2024-09-12 13:05:55,280 Writing html report.\n2024-09-12 13:05:55,354 Finished!\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "10 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "10.0000000"}, {"title": "Job End Time", "value": "2024-09-12 13:05:55", "plugin": "core", "name": "end_epoch", "raw_value": "1726146355.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 13:05:45", "plugin": "core", "name": "start_epoch", "raw_value": "1726146345.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "nanoplot/1.43.0+galaxy0-2", "has_data": true, "data": {"tool_id": "nanoplot", "tool_version": "1.43.0+galaxy0", "test_index": 2, "time_seconds": 30.351978063583374, "inputs": {"mode|reads|files": [{"src": "hda", "id": "98e036e4ea2088a4"}, {"src": "hda", "id": "24cfce1dc6c71df2"}], "mode|reads|type": "fasta", "mode|choice": "combined"}, "job": {"model_class": "Job", "id": "77906ef2693d8471", "state": "error", "exit_code": null, "update_time": "2024-09-12T13:06:36.861985", "create_time": "2024-09-12T13:06:25.039233", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.43.0+galaxy0", "history_id": "45fb41c325e9adff", "external_id": "gxy-h46l9", "command_line": "ln -s '/galaxy/server/database/objects/9/a/1/dataset_9a140251-4c09-4678-ab00-95f3d6a2785c.dat' './read_0.fasta' && ln -s '/galaxy/server/database/objects/d/a/d/dataset_dad0eec8-6d14-484e-a2f4-b6b7adaff47a.dat' './read_1.fasta' && NanoPlot --threads ${GALAXY_SLOTS:-4} --tsv_stats --no_static --fasta read_0.fasta read_1.fasta -o '.' && >&2 cat *log", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "customization": "{\"N50\": false, \"color\": null, \"plots\": null}", "filter": "{\"alength\": false, \"barcoded\": false, \"downsample\": \"\", \"drop_outliers\": false, \"loglength\": false, \"maxlength\": \"\", \"minlength\": \"\", \"minqual\": \"\", \"no_supplementary\": false, \"percentqual\": false, \"readtype\": null, \"runtime_until\": \"\"}", "mode": "{\"__current_case__\": 1, \"choice\": \"combined\", \"reads\": {\"__current_case__\": 1, \"files\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}, {\"id\": 135, \"src\": \"hda\"}]}, \"type\": \"fasta\"}}"}, "inputs": {"mode|reads|files": {"id": "98e036e4ea2088a4", "src": "hda", "uuid": "9a140251-4c09-4678-ab00-95f3d6a2785c"}, "mode|reads|files1": {"id": "98e036e4ea2088a4", "src": "hda", "uuid": "9a140251-4c09-4678-ab00-95f3d6a2785c"}, "mode|reads|files2": {"id": "24cfce1dc6c71df2", "src": "hda", "uuid": 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"poretools_extract", "tool_version": "0.6.1a1.0", "test_index": 0, "time_seconds": 11.22337007522583, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "poretools_extract/0.6.1a1.0-1", "has_data": true, "data": {"tool_id": "poretools_extract", "tool_version": "0.6.1a1.0", "test_index": 1, "time_seconds": 56.394981384277344, "inputs": {"input": {"src": "hda", "id": "2ba83b5637b11a77"}, "output_format": "fasta"}, "job": {"model_class": "Job", "id": "2c14ff1b8ee62486", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T13:07:45.368130", "create_time": "2024-09-12T13:07:08.643572", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0", "history_id": "45fb41c325e9adff", "external_id": "gxy-l7bff", "command_line": "poretools fasta --type all --min-length 0 --max-length 1000000000 '/galaxy/server/database/objects/0/2/0/dataset_02080b6e-0f9b-470d-b5d3-4fe0c1d76606.dat' > '/galaxy/server/database/objects/c/c/2/dataset_cc2791c3-e807-425c-aa87-9bee2c1293eb.dat'", "traceback": null, "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "end": "\"\"", "start": "\"\"", "group": "\"\"", "quality": "\"\"", "type": "\"all\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "output_format": "\"fasta\""}, "inputs": {"input": {"id": "2ba83b5637b11a77", "src": "hda", "uuid": "02080b6e-0f9b-470d-b5d3-4fe0c1d76606"}}, "outputs": {"output": {"id": "3182a5404b7e43fc", "src": "hda", "uuid": "cc2791c3-e807-425c-aa87-9bee2c1293eb"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 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"tool_version": "3.3.2", "test_index": 1, "time_seconds": 0.10469770431518555, "execution_problem": "Input staging problem: Test input file (customers.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-10", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 10, "time_seconds": 0.10558342933654785, "execution_problem": "Input staging problem: Test input file (netMHC_summary.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-11", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 11, "time_seconds": 0.1053917407989502, "execution_problem": "Input staging problem: Test input file (math_input.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-2", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 2, "time_seconds": 0.10482430458068848, "execution_problem": "Input staging problem: Test input file (customers.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-3", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 3, "time_seconds": 0.10566020011901855, "execution_problem": "Input staging problem: Test input file (IEDB.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-4", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 4, "time_seconds": 0.10706710815429688, "execution_problem": "Input staging problem: Test input file (testdb.sqlite) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-5", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 5, "time_seconds": 0.10654973983764648, "execution_problem": "Input staging problem: Test input file (pets.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-6", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 6, "time_seconds": 0.10609865188598633, "execution_problem": "Input staging problem: Test input file (psm_report.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-7", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 7, "time_seconds": 0.10585260391235352, "execution_problem": "Input staging problem: Test input file (psm_report.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-8", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 8, "time_seconds": 0.10671734809875488, "execution_problem": "Input staging problem: Test input file (psm_report.tsv) cannot be found.", "status": "error"}}, {"id": "query_tabular/3.3.2-9", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.2", "test_index": 9, "time_seconds": 0.10695528984069824, "execution_problem": "Input staging problem: Test input file (netMHC_summary.tsv) cannot be found.", "status": "error"}}, {"id": "samtools_mpileup/2.1.7-0", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.7", "test_index": 0, "time_seconds": 41.50771403312683, "inputs": {"input": [{"src": "hda", "id": "fd2eba97839297b7"}, {"src": "hda", "id": "3cad2cf35f5d9343"}, {"src": "hda", "id": "41674f4dd3174743"}], "addref_cond|ref": {"src": "hda", "id": "95852cd1d8428b7e"}, "addref_cond|addref_select": "history", "advanced_options|limit_by_region|region_paste": "17:100-150", "advanced_options|limit_by_region|limit_by_regions": "limit", "advanced_options|advanced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "2e58c3969419a55a", "state": "ok", "exit_code": 0, "update_time": "2024-09-12T12:59:01.998278", "create_time": "2024-09-12T12:58:47.554824", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.16)", "copied_from_job_id": null, "tool_id": 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